This is a comprehensive, multi-scale model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins and their post-translational modifications sites, and over 1,000 biochemical interactions. The model also contains a number of commonly expressed receptor signaling pathways, including ErbB (1-4), EGFR endocytosis and recycling, G-protein-coupled receptor (alpha i, alpha q, alpha 12/13, and alpha s ligands), integrin, e-cadherin, and stress pathways. Helikar Tomas thelika@unmc.edu University of Nebraska - Lincoln 2012-04-10T12:46:49Z 2016-01-22T07:08:46Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q13009">Q13009</a>

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<div style="font-style: normal;"><font face="Georgia" size="2"><br/></font></div><div><font face="Georgia" size="2">Actin (<em>Homo sapiens</em>)</font></div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P60709" style="font-style: normal; text-decoration: none; background-color: rgb(255, 255, 255);">P60709</a></font><div><font face="Georgia" size="2">Gene Name: ACTB </font></div><div><font face="Georgia" size="2">Gene ID: 60<br/></font><div style="font-style: normal;"><font face="Georgia" size="2"><br/></font></div><div style="font-style: normal;"><font face="Georgia" size="2">In "Guard Cell Abscisic Acid Signaling", this node represents actin cytoskeleton reorganization of plant guard cells [1]. </font></div><div style="font-style: normal;"><font face="Georgia" size="2">Actin (<em class="tax" style="line-height: 1.5;">Arabidopsis thaliana)</em></font></div><div style="font-style: normal;"><font face="Georgia" size="2"> UniProt ID: <a href="http://www.uniprot.org/uniprot/P53497" style="text-decoration: none; background-color: rgb(255, 255, 255);">P53497</a></font></div><div style="font-style: normal;"><font face="Georgia" size="2">Gene Name: ACT12</font></div><div style="font-style: normal;"><font face="Georgia" size="2">Gene ID: <span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;">823805</span></font></div></div>

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<font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase kinase kinase 3 [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span></font><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q99759" style="font-size: small; text-decoration: none; background-color: rgb(255, 255, 255);">Q99759</a></font></div><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/4215" ref="ordinalpos=3&ncbi_uid=4215&link_uid=4215" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP3K3</a></font></div><div><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia">Gene ID: 4215</font></span></div>

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Uniprot ID: P50148

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<font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase 14 </span><br/></font><div><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">Q16539</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/1432" ref="ordinalpos=1&ncbi_uid=1432&link_uid=1432" style="line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAPK14</a></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene ID: </span><span style="background-color: rgb(255, 255, 255); line-height: 17.999801635742188px;">1432</span></font></div>

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<span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">auxilin2</span>

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<span style="color: rgb(84, 84, 84); font-family: arial, sans-serif; font-size: small; line-height: 20.22222328186035px; background-color: rgb(255, 255, 255);">ADP ribosylation factor family of GTP-binding proteins</span>

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

<font style="line-height: normal; background-color: rgb(255, 255, 255);" face="Georgia" size="2"><span style="border: 0px; outline: 0px; font-style: inherit; font-variant: inherit; line-height: inherit; vertical-align: baseline; margin: 0px; padding: 0px;">Diacylglycerol </span></font><div><font face="Georgia" size="2">PubChem ID: <span style="line-height: 19px; background-color: rgb(255, 255, 255);">6026790</span></font></div><div><font face="Georgia" size="2"><span style="line-height: inherit; font-style: inherit; font-variant: inherit; border: 0px; outline: 0px; vertical-align: baseline; margin: 0px; padding: 0px;">Molecular Formula:</span><span style="background-color: rgb(255, 255, 255); line-height: inherit;"> </span><span style="background-color: rgb(255, 255, 255); line-height: inherit;">C</span><sub style="font-style: inherit; font-variant: inherit; border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px;">37</sub><span style="background-color: rgb(255, 255, 255); line-height: inherit;">H</span><sub style="font-style: inherit; font-variant: inherit; border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px;">70</sub><span style="background-color: rgb(255, 255, 255); line-height: inherit;">O</span><sub style="font-style: inherit; font-variant: inherit; border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px;">5</sub><span style="background-color: rgb(255, 255, 255); line-height: inherit;">   </span><span style="line-height: inherit; font-style: inherit; font-variant: inherit; border: 0px; outline: 0px; vertical-align: baseline; margin: 0px; padding: 0px;">Molecular Weight:</span><span style="background-color: rgb(255, 255, 255); line-height: inherit;"> </span><span style="background-color: rgb(255, 255, 255); line-height: inherit;">594.9487  </span></font></div>

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<font size="2" style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; background-color: rgb(255, 255, 255);" face="Georgia">Growth factor receptor-bound protein 2</font><div><font face="Georgia" style="background-color: rgb(255, 255, 255);"><font size="2" style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">Uniprot Accession ID: </font><font size="2">Q60631</font></font></div><div><font face="Georgia" size="2" style="background-color: rgb(255, 255, 255);">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/2885" ref="ordinalpos=1&ncbi_uid=2885&link_uid=2885" style="line-height: 18.88888931274414px; white-space: nowrap;"><span class="highlight">GRB2</span></a></font></div><div><font size="2" face="Georgia" style="background-color: rgb(255, 255, 255);">Gene ID: 2885</font></div>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q13177">Q13177</a><div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q13153" style="font-size: 10pt;">Q13153</a></div>

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<table border="0" cellpadding="0" cellspacing="0" width="964" style="border-collapse:\r\n collapse;width:723pt"><tbody><tr height="20" style="height:15.0pt">\r\n <td height="20" class="xl65" width="964" style="height:15.0pt;width:723pt">G\r\n protein-coupled receptor kinase (unspecified)<br/>UniProt ID: <a href="http://www.uniprot.org/uniprot/P32298" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">P32298</a><br/>Gene Name: GIT1<br/>Gene ID: <span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">28964</span></td></tr></tbody></table>

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<font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase kinase 3 [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span><br/></font><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/P46734" style="font-size: small; text-decoration: none; background-color: rgb(255, 255, 255);">P46734</a></font></div><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/5606" ref="ordinalpos=4&ncbi_uid=5606&link_uid=5606" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP2K3</a></font></div><div><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia">Gene ID: 5606</font></span></div>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/P42768" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P42768</a>

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<font size="2">There are several different individual d<span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">iacylglycerol kinases. </span></font><div><ul><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase alpha, UniProt ID: </span><span style="font-family: sans-serif; background-color: rgb(255, 255, 255);">P23743</span></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase beta, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">Q9Y6T7</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase gamma, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">P49619</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase delta, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">Q16760</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase epsilon, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">P52429</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase zeta, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">Q13574</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase eta, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">Q86XP1</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase theta, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">P52824</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase iota, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">O75912</span></font></font></li><li><font size="2"><span style="font-family: sans-serif; line-height: 16px; background-color: rgb(255, 255, 255);">Diacylglycerol kinase kappa, UniProt ID: </span><font face="sans-serif"><span style="background-color: rgb(255, 255, 255);">Q5KSL6</span></font></font></li></ul></div>

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Cool/Pix proteins

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<font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">PP2A consists of a common heterodimeric core enzyme, composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits [10]. </span><span style="line-height: 16px; background-color: rgb(255, 255, 255);">Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules [10]. </span></font><div><font face="Georgia" size="2">Catalytic subunit: </font></div><div><span style="line-height: 19.49652862548828px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">protein phosphatase 2, catalytic subunit, alpha isozyme</font></span></div><div><font face="Georgia" size="2"><span style="line-height: 19.49652862548828px; background-color: rgb(255, 255, 255);">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">P67775</span></font></div><div><span style="line-height: 19.49652862548828px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Gene Name: PPP2CA</font></span></div><div><font size="2" face="Georgia"><span style="line-height: 19.488636016845703px;">NCBI Gene ID: 5515</span></font></div><div><div style="font-weight: normal; font-family: Arial, Verdana; font-size: 10pt; line-height: normal;"><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);"><br/></span></div></div>

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<div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">Ras-like Protein</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">UniProt Accession ID: <a href="http://www.uniprot.org/uniprot/P0CQ42">P0CQ42</a></font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2"><br/></font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">v-Ha-ras Harvey rat sarcoma viral oncogene homolog (HRAS)</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">Rat:</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">UniProt Accession ID: P20171</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font size="2" face="Georgia">Human:</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font size="2" face="Georgia">UniProt Accession ID: P01112</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font size="2" face="Georgia">Gene Name: HRAS</font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2">Gene ID: <span style="background-color: rgb(255, 255, 255); color: rgb(87, 87, 87); line-height: 16.78819465637207px; white-space: nowrap;">3265</span></font></div><div style="font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2"><br/></font></div><div><span style="font-weight: normal;"><font face="Georgia" size="2">Kirsten rat sarcoma viral oncogene homolog (KRAS)</font></span></div><div><font face="Georgia" size="2"><span style="font-weight: normal;">UniProt ID: </span><strong style="background-color: rgb(255, 255, 255);">P01116</strong></font></div><div><span style="font-weight: normal;"><font face="Georgia" size="2">Gene Name: KRAS</font></span></div><div><font face="Georgia" size="2"><span style="font-weight: normal;">Gene ID: </span><span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;">3845</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;"><br/></span></font></div><div>NRAS = neuroblastoma RAS viral (v-ras) oncogene homolog </div><div>UniProt ID: <a href="http://www.uniprot.org/uniprot/P01111" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">P01111</a></div><div>Gene Name: NRAS</div><div>Gene ID: <span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">4893</span></div>

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Phosphatidylinositol (3,4)-biphosphate.

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

<div><span style="border: 0px; outline: 0px; vertical-align: baseline; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255); line-height: 17px;"><font size="2" face="Georgia">Phosphatidic acid</font></span></div><div style="font-style: normal; font-variant: normal; line-height: normal;"><font face="Georgia" size="2"><span style="border: 0px; outline: 0px; line-height: 17px; vertical-align: baseline; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">PubChem ID: </span><a name="cid2entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=5460104[uid]" style="border: 0px; outline: 0px; line-height: 19px; vertical-align: baseline; margin: 0px; padding: 0px; text-decoration: none; background-color: rgb(255, 255, 255);">5460104</a><span style="line-height: 19px; background-color: rgb(255, 255, 255);"><br/></span><span style="border: 0px; outline: 0px; line-height: 17px; vertical-align: baseline; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">Molecular Formula:</span><span style="line-height: 17px; background-color: rgb(255, 255, 255);"> C</span><sub style="border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">5</sub><span style="line-height: 17px; background-color: rgb(255, 255, 255);">H</span><sub style="border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">9</sub><span style="line-height: 17px; background-color: rgb(255, 255, 255);">O</span><sub style="border: 0px; outline: 0px; line-height: 0; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">8</sub><span style="line-height: 17px; background-color: rgb(255, 255, 255);">P   </span><span style="border: 0px; outline: 0px; line-height: 17px; vertical-align: baseline; margin: 0px; padding: 0px; background-color: rgb(255, 255, 255);">Molecular Weight:</span><span style="line-height: 17px; background-color: rgb(255, 255, 255);"> 228.093922</span></font></div>

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

Fer kinase

2015-11-15T16:30:59Z

<span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Mitogen-activated protein kinase kinase 7</font></span><div><font face="Georgia" size="2"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/O14733" style="text-decoration: none; background-color: rgb(255, 255, 255);">O14733</a></font></div><div><font face="Georgia" size="2"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/5609" ref="ordinalpos=3&ncbi_uid=5609&link_uid=5609" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP2K7</a></font></div><div><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Gene ID: 5609</font></span></div>

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<div><font face="Arial, Verdana" style="font-size: 10pt;">C-terminal Src kinase</font></div><font face="Arial, Verdana" size="2"><br/><font size="2">Csk regulation <font size="2">has been reviewed in [18]</font></font><br/></font><div><font face="Arial, Verdana" size="2"><font size="2"><font size="2"><br/></font></font></font></div><div><font face="Arial, Verdana">Uniprot ID: </font><a href="http://www.uniprot.org/uniprot/P41240" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">P41240</a></div>

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<span style="color: rgb(64, 56, 56); font-family: 'Lucida Sans Unicode', Arial, 'Lucida Grande', Tahoma, Verdana, Helvetica, sans-serif; line-height: 19.200000762939453px; text-align: justify; background-color: rgb(255, 255, 255);">membrane-anchored scaffold protein for Csk</span>

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Uniprot ID: Q16566

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<div><font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Son of sevenless homolog 1 (Drosophila) [</span><em style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><span class="highlight">Homo</span> sapiens</em><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span></font></div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q07889">Q07889</a></font><div><font face="Georgia" size="2">Gene Name:<a href="http://www.ncbi.nlm.nih.gov/gene/6654" ref="ordinalpos=1&ncbi_uid=6654&link_uid=6654" style="line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">SOS1</a></font></div><div><font face="Georgia" size="2">Gene ID: 6654</font></div><div><font face="Georgia" size="2"><br/></font></div><div><font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Son of sevenless homolog 2 (Drosophila) [</span><em style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><span class="highlight">Homo</span> sapiens</em><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span><br/></font><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q07890">Q07890</a></font></div></div><div><div><font face="Georgia" size="2">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/6655" ref="ordinalpos=2&ncbi_uid=6655&link_uid=6655" style="line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">SOS2</a></font></div><div><font face="Georgia" size="2">Gene ID:6655</font></div></div>

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<font face="Georgia" size="2">Src homology 2 domain containing transforming protein 1</font><div><font face="Georgia" size="2">UniProt ID:<span style="background-color: rgb(255, 255, 255);">P29353</span></font></div><div><font face="Georgia" size="2">Gene Name: SHC1</font></div><div><font face="Georgia" size="2">Gene ID: <span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;">6464</span></font></div>

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Phosphatidylinositol (3,4,5)-triphosphate.

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<div><font face="Georgia" size="2"><span class="highlight" style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">NCK</span><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"> adaptor protein 1</span></font></div><div><font face="Georgia" size="2">UniProt ID: <a href="http://www.uniprot.org/uniprot/P16333" style="text-decoration: none; background-color: rgb(255, 255, 255);">P16333</a></font></div><div><font face="Georgia" size="2">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/4690" ref="ordinalpos=2&ncbi_uid=4690&link_uid=4690" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">NCK1</a></font></div><div><font face="Georgia" size="2">Gene ID: 4690</font></div>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/P18613" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P18613</a>

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<table border="0" cellpadding="0" cellspacing="0" width="964" style="border-collapse:\r\n collapse;width:723pt"><tbody><tr height="20" style="height:15.0pt">\r\n <td height="20" class="xl65" width="964" style="height:15.0pt;width:723pt">Beta-adrenergic\r\n receptor kinase 1<br/>UniProt ID: <a href="http://www.uniprot.org/uniprot/P25098" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">P25098</a><br/>Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/156" ref="ordinalpos=2&ncbi_uid=156&link_uid=156" style="color: rgb(100, 42, 143); font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; white-space: nowrap; background-color: rgb(213, 222, 227);">ADRBK1</a><br/>Gene ID: <span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">156</span></td></tr></tbody></table>

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Uniprot ID: Q14643

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q15759">Q15759</a><div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/P45983" style="font-size: 10pt;">P45983</a></div>

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<font face="Georgia" style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">v-</span><span class="highlight" style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">akt</span><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"> murine thymoma viral oncogene homolog 1 [</span><em style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">(human)]</span></font><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/P31749" style="text-decoration: none; background-color: rgb(255, 255, 255);">P31749</a></font></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><font face="Georgia" size="2"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/207" ref="ordinalpos=1&ncbi_uid=207&link_uid=207" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">AKT1</a></font></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Gene ID: 207</font></span></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2"><br/></font></span></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Additions from the MAPK Network:</font></span></div><div><span style="background-color: rgb(255, 255, 255);"><font face="Georgia" size="2"></font></span><div><br/></div><div><span style="line-height: 18.8888893127441px;">AKT2 = v-akt murine thymoma viral oncogene homolog 2</span></div><div><div><span style="line-height: 18.8888893127441px;">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/P31751" style="font-size: 13px; text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; line-height: 20.081974029541px;">P31751</a></div><div><span style="line-height: 18.8888893127441px;">Gene Name: AKT2</span></div><div><span style="line-height: 18.8888893127441px;">Gene ID: 208</span></div></div><div><span style="line-height: 18.8888893127441px;"><br/></span></div><div><span style="line-height: 18.8888893127441px;">AKT3 = v-akt murine thymoma viral oncogene homolog 3</span></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: 18.8888893127441px;"><div style="font-family: Georgia; font-size: small; line-height: normal;"><span style="line-height: 18.8888893127441px;">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q9Y243" style="font-size: 10pt; text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; line-height: 20.081974029541px; background-color: rgb(222, 239, 245);">Q9Y243</a></div><div style="font-family: Georgia; font-size: small; line-height: normal;"><span style="line-height: 18.8888893127441px;">Gene Name: AKT3</span></div><div style="font-family: Georgia; font-size: small; line-height: normal;"><span style="line-height: 18.8888893127441px;">Gene ID: 10000</span></div></div></div>

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Phosphatidylinositol 4-phosphate 5-kinase.<div><br/></div>

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<font face="Georgia" size="2">There are three forms of IP3:</font><div><ul><li><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">Inositol-trisphosphate 3-kinase A, UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">P23677 (activated by calmodulin [3]). </span></font></li><li><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">Inositol-trisphosphate 3-kinase B, </span><span style="background-color: rgb(255, 255, 255); line-height: 16px;">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">P27987</span><span style="background-color: rgb(255, 255, 255); line-height: 16px;">  (more sensitive, by 8-fold, to calmodulin than isoform A [4])</span></font></li><li><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">Inositol-trisphosphate 3-kinase C, UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">Q96DU7 (activated by calmodulin like IP3A [2], but localized and expressed h</span><span style="background-color: rgb(255, 255, 255); line-height: 16px;">ighly in pancreas, skeletal muscle, liver, placenta and weakly in kidney and brain [2].</span><span style="background-color: rgb(255, 255, 255);"> </span><span style="line-height: 16px; background-color: rgb(255, 255, 255);">Shuttles actively between nucleus and cytoplasm with both nuclear import and nuclear export activity. [1])</span></font></li></ul></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">In EGFR ErbB Signaling  and IL-6 models, this node represents the molecule i</span>nositol-1,4,5-triphosphate (PubChem ID:<span style="color: rgb(85, 85, 85); line-height: 19px; background-color: rgb(255, 255, 255);"> </span><a name="cid2entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=439456[uid]" style="border: 0px; outline: 0px; line-height: 19px; vertical-align: baseline; margin: 0px; padding: 0px; text-decoration: none; color: rgb(0, 86, 204); background-color: rgb(255, 255, 255);">439456</a>) and not the kinase [5,6]. </font></div>\r\n \r\n \r\n \r\n <div class="page" title="Page 2">\r\n <div class="section">\r\n <div class="layoutArea">\r\n <div class="column">\r\n <p><span style="font-size: 10.000000pt; font-family: 'Helvetica'"> <br/></span></p>\r\n </div>\r\n </div>\r\n </div>\r\n </div>

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E3 ligase

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Phosphatidylinositol-4,5-biphosphate.

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<span style="line-height: 16px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Mitogen-activated protein kinase kinase kinase 1</font></span><div><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">Q13233</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/4214" ref="ordinalpos=1&ncbi_uid=4214&link_uid=4214" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP3K1</a></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene ID: 4214</span></font></div>

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<div><span style="line-height: 16px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">3-phosphoinositide-dependent protein kinase 1</font></span></div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q15118">Q15118</a></font><div><font face="Georgia" size="2">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/5170" ref="ordinalpos=1&ncbi_uid=5170&link_uid=5170" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);"><span class="highlight">PDPK1</span></a></font></div><div><font face="Georgia" size="2">Gene ID: 5170</font></div>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/P56945" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P56945</a>

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<div><font face="Georgia" size="2" style="line-height: 14.390625px; background-color: rgb(255, 255, 255);">Ribosomal protein </font><font face="Georgia" size="2" style="line-height: 14.390625px; background-color: rgb(255, 255, 255);">S6 kinase, 90kDa polypeptide 1</font></div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q9UK32" style="text-decoration: none; background-color: rgb(255, 255, 255);">Q9UK32</a></font><div><font face="Georgia" size="2">Gene Name: </font><a href="http://www.ncbi.nlm.nih.gov/gene/6195" ref="ordinalpos=1&ncbi_uid=6195&link_uid=6195" style="color: rgb(100, 42, 143); font-family: arial, helvetica, clean, sans-serif; font-size: 13.333333969116211px; line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">RPS6KA1</a></div><div><font face="Georgia" size="2">Gene ID: 6195</font></div>

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<font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Cell division cycle 42 [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span></font><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/P60953" style="font-size: small; text-decoration: none; background-color: rgb(255, 255, 255);">P60953</a></font></div><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/998" ref="ordinalpos=1&ncbi_uid=998&link_uid=998" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);"><span class="highlight">CDC42</span></a></font></div><div><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia">NCBI Gene ID: 998</font></span></div>

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<font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Protein tyrosine kinase 2 [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><span class="highlight">Homo</span> sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span></font><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q05397" style="font-size: small; text-decoration: none; background-color: rgb(255, 255, 255);">Q05397</a></font></div><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/5747" ref="ordinalpos=1&ncbi_uid=5747&link_uid=5747" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">PTK2</a></font></div><div><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia">Gene ID: 5747</font></span></div>

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Vinculin

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q13393">Q13393</a><br/><div><span style="font-size: 10pt;">Uniprot ID: </span><a href="http://www.uniprot.org/uniprot/O14939" style="font-size: 10pt;">O14939</a></div><div><span style="font-size: 10pt;">Uniprot ID: </span><a href="http://www.uniprot.org/uniprot/Q8N7P1" style="font-size: 10pt;">Q8N7P1</a></div><div><span style="font-size: 10pt;">Uniprot ID: </span><a href="http://www.uniprot.org/uniprot/Q8IV08" style="font-size: 10pt;">Q8IV08</a></div><div><span style="font-size: 10pt;">Uniprot ID: </span><a href="http://www.uniprot.org/uniprot/Q8N2A8" style="font-size: 10pt;">Q8N2A8</a></div><div><span style="font-size: 10pt;">Uniprot ID:</span> <a href="http://www.uniprot.org/uniprot/Q96BZ4" style="font-size: 10pt;">Q96BZ4</a></div>

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<div style="font-size: 10pt;">mitogen-activated protein kinase <span style="font-size: 10pt;">kinase 1</span></div><div style="font-size: 10pt;"><span style="font-size: 10pt;"><br/></span></div><div style="font-size: 10pt;">MAP2K5:</div><div style="font-size: 10pt;">UniProt Accession ID: Q13163</div><div style="font-size: 10pt;"><br/></div><div style="font-size: 10pt;">MAP2K6:</div><div style="font-size: 10pt;">UniProt Accession ID: P52564 </div><div style="font-size: 10pt;"><br/></div><div style="font-size: 10pt;">MAP2K3:</div><div style="font-size: 10pt;">UniProt Accession ID: P46734 </div><div style="font-size: 10pt;"><br/></div><div style="font-size: 10pt;">MAP2K1:</div><div style="font-size: 10pt;">UniProt Accession ID: Q02750</div><div style="font-size: 10pt;"><br/></div><div><font size="2">MAP2K2:</font></div><div><font size="2">UniProt Accession ID: P36507</font></div>

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<font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase kinase kinase 14 [</span><em style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span></font><div style="line-height: normal;"><font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q99558" style="text-decoration: none; background-color: rgb(255, 255, 255);">Q99558</a></font></div><div style="line-height: normal;"><font face="Georgia" size="2"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/9020" ref="ordinalpos=3&ncbi_uid=9020&link_uid=9020" style="color: rgb(100, 42, 143); line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP3K14</a></font></div><div><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">NCBI Gene ID: 9020</font></span></div>

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<div><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Mitogen-activated protein kinase kinase kinase 4</font></span></div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q9Y6R4">Q9Y6R4</a></font><div><font face="Georgia" size="2">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/4216" ref="ordinalpos=1&ncbi_uid=4216&link_uid=4216" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP3K4</a> </font></div><div><font face="Georgia" size="2">Gene ID: 4216<br/><br/>Also known as Mekk4</font></div>

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<font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Dedicator of cytokinesis 1 [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span></font><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q14185" style="font-size: small; text-decoration: none; background-color: rgb(255, 255, 255);">Q14185</a></font></div><div><font face="Georgia"><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/1793" ref="ordinalpos=2&ncbi_uid=1793&link_uid=1793" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">DOCK1</a></font></div><div><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><font face="Georgia">Gene ID: 1793</font></span></div>

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<div><table border="0" cellpadding="0" cellspacing="0" width="964" style="border-collapse:\r\n collapse;width:723pt"><tbody><tr height="20" style="height:15.0pt">\r\n <td height="20" class="xl65" width="964" style="height:15.0pt;width:723pt">v-crk\r\n sarcoma virus CT10 oncogene homolog</td></tr></tbody></table></div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/P07333" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P07333</a><div>Gene Name: CRK</div><div>Gene ID: <span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">1398</span></div>

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<span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">GRB2-associated binding protein 1 </font></span><div><font face="Georgia" size="2" style="background-color: rgb(255, 255, 255);"><span style="line-height: 18.88888931274414px;">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/Q13480" style="text-decoration: none;">Q13480</a></font></div><div><font face="Georgia" size="2" style="background-color: rgb(255, 255, 255);"><span style="line-height: 18.88888931274414px;">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/2549" ref="ordinalpos=1&ncbi_uid=2549&link_uid=2549" style="line-height: 18.88888931274414px; white-space: nowrap;"><span class="highlight">GAB1</span></a></font></div><div><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Gene ID: 2549</font></span></div>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q9NQ66">Q9NQ66</a>

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Adapter protein 2

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/P15153">P15153</a><div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/P31749" style="font-size: 10pt;">P31749</a></div><div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/P60763" style="font-size: 10pt;">P60763</a></div>

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<div><span style="font-family: Georgia; font-size: small;">Phospholipase C, gamma 1 (PLCG1)</span></div><div><font face="Georgia" size="2">UniProt Accession ID:</font><span style="font-size: 10pt;"> </span><a href="http://www.uniprot.org/uniprot/P19174" style="font-size: 10pt;">P19174</a></div><div><font size="2" face="Georgia">Gene Name: PLCG1</font></div><div><font size="2" face="Georgia">NCBI Gene ID: 5535</font></div>

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Uniprot ID: P61160

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<div><font face="Georgia"><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Zinc fingers and homeoboxes 2 [</span><em style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"><span class="highlight">Homo</span>sapiens</em><span style="line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (human)]</span></font></div><font face="Georgia">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P04049">P04049</a></font><div><font face="Georgia">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/22882" ref="ordinalpos=1&ncbi_uid=22882&link_uid=22882" style="font-size: 10pt; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">ZHX2</a></font></div><div><font face="Georgia">Gene ID: <span style="background-color: rgb(255, 255, 255); font-size: 12.222222328186035px; line-height: 17.999801635742188px;">22882</span></font></div>

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Beta Parvin

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<div>Cyclic AMP</div>Uniprot ID: <a href="http://www.uniprot.org/uniprot/P49913" style="text-decoration: none; font-family: sans-serif; font-size: small; background-color: rgb(255, 255, 255);">P49913</a>

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Uniprot ID: P20339

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<font face="Georgia" size="2">Phosphatase and tensin homolog</font><div><font face="Georgia" size="2">Also known as: <span style="background-color: rgb(255, 255, 255); line-height: 16px;">Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255); line-height: 16px;">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">P60484</span></font></div><div><span style="background-color: rgb(255, 255, 255); line-height: 16px;"><font face="Georgia" size="2">Gene Name: PTEN</font></span></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255); line-height: 16px;">NCBI Gene ID: </span><span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;">5728</span></font></div>

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<span style="line-height: 16px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Tyrosine-protein phosphatase non-receptor type 11</font></span><div><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">Q06124</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene Name: </span><span style="background-color: rgb(255, 255, 255); line-height: 19.49652862548828px;">PTPN11</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene ID: </span><span style="background-color: rgb(255, 255, 255); line-height: 18.88888931274414px;">5781</span></font></div>

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<div><font face="Georgia"><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Integrin</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">, </span><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">alpha 5</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(fibronectin receptor, alpha polypeptide) [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span></font></div><font face="Georgia"><font size="2" style="font-size: 10pt;">Uniprot ID: </font><span style="font-size: small;">P08648 </span></font><div><font face="Georgia"><font size="2">Gene Name: </font><a href="http://www.ncbi.nlm.nih.gov/gene/3678" ref="ordinalpos=1&ncbi_uid=3678&link_uid=3678" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">ITGA5</a></font></div><div><font size="2" face="Georgia">Gene ID: 3678<br/></font><div style="font-size: 10pt;"><span style="font-size: small;"><font face="Georgia"><br/></font></span></div><div style="font-size: 10pt;"><font face="Georgia"><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Integrin</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">, </span><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">beta 7</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">[</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span></font></div><div style="font-size: 10pt;"><span style="font-size: small;"><font face="Georgia">Uniprot ID: P26010 </font></span></div><div style="font-size: 10pt;"><font face="Georgia"><span style="font-size: small;">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/3695" ref="ordinalpos=2&ncbi_uid=3695&link_uid=3695" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">ITGB7</a></font></div><div style="font-size: 10pt;"><span style="font-size: small;"><font face="Georgia">Gene ID: 3695</font></span></div><div style="font-size: 10pt;"><span style="font-size: small;"><font face="Georgia"><br/></font></span></div><div style="font-size: 10pt;"><font face="Georgia"><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Integrin</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">, </span><span class="highlight" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">beta 1</span><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);"> (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [</span><em style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; background-color: rgb(255, 255, 255);">(human)]</span></font></div><div style="font-size: 10pt;"><span style="font-size: small;"><font face="Georgia">Uniprot ID: P05556</font></span></div><div><font face="Georgia"><font size="2">Gene Name: </font><a href="http://www.ncbi.nlm.nih.gov/gene/3688" ref="ordinalpos=2&ncbi_uid=3688&link_uid=3688" style="font-size: 13.333333969116211px; line-height: 19.999780654907227px; white-space: nowrap; background-color: rgb(255, 255, 255);">ITGB1</a></font></div><div><font size="2" face="Georgia">Gene ID: 3688</font></div></div>

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<span style="line-height: 16px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Mitogen-activated protein kinase kinase kinase 11</font></span><div><font face="Georgia" size="2"><span style="line-height: 16px; background-color: rgb(255, 255, 255);">UniProt ID: </span><span style="background-color: rgb(255, 255, 255);">Q16584</span></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/4296" ref="ordinalpos=2&ncbi_uid=4296&link_uid=4296" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP3K11</a></font></div><div><font face="Georgia" size="2"><span style="background-color: rgb(255, 255, 255);">Gene ID: 4296</span></font></div>

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<span style="color: rgb(64, 56, 56); font-family: Arial, 'Liberation Sans', sans-serif; line-height: 19.200000762939453px; background-color: rgb(255, 255, 255);">ubiquitin isopeptidase Y</span>

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Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q9Y490">Q9Y490</a>

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<font face="Arial, Verdana" size="2" style="font-weight: normal; font-size: 10pt;">phosphoinositide-3-kinase</font><div><font size="2" style="font-weight: normal;"><br/></font><div style="font-weight: normal;"><font size="2">catalytic, alpha polypeptide (PIK3CA)</font></div><div style="font-weight: normal;"><font size="2">UniProt Accession ID: P42336</font></div><div style="font-weight: normal;"><font size="2"><br/></font></div><div><div style="font-weight: normal;"><font size="2">catalytic, beta polypeptide (PIK3CB)</font></div><div style="font-weight: normal;"><font size="2">UniProt Accession ID: Q6PJ60</font></div><div style="font-weight: normal;"><font size="2"><br/></font></div><div style="font-weight: normal;"><div><font size="2">catalytic, gamma polypeptide (PIK3CG)</font></div><div><font size="2">UniProt Accession ID: P48736</font></div></div><div style="font-weight: normal;"><font size="2"><br/></font></div><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">Phosphoinositide 3-kinase regulatory subunit 6</span></div><div style="font-weight: normal; font-size: 10pt;"><font face="Arial, Verdana" size="2">UniProt Accession ID: </font><a href="http://www.uniprot.org/uniprot/Q5UE93" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">Q5UE93</a></div><div style="font-weight: normal; font-size: 10pt;"><br/></div><div style="font-size: 10pt;"><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta</span></div><div style="font-weight: normal; font-size: 10pt;">UniProt Accession ID: <a href="http://www.uniprot.org/uniprot/O00750" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">O00750</a></div><div style="font-weight: normal; font-size: 10pt;"><br/></div><div style="font-size: 10pt;"><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha</span></div><div style="font-weight: normal; font-size: 10pt;">UniProt Accession ID: <a href="http://www.uniprot.org/uniprot/O00443" style="font-size: small; text-decoration: none; font-family: sans-serif; background-color: rgb(255, 255, 255);">O00443</a></div></div></div>

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MAP3K7 = mitogen-activated protein kinase kinase kinase 7<div>UniProt ID: <a href="http://www.uniprot.org/uniprot/O43318" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">O43318</a></div><div>Gene Name: MAP3K7</div><div>Gene ID: <span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">6885</span></div>

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<div><span style="font-size: 10pt;">Also known as MKK4 or MAP2K4.</span></div><div><span style="font-size: 10pt;"><br/></span></div><div><span style="font-size: 10pt;">Uniprot ID: </span><a href="http://www.uniprot.org/uniprot/P45985" style="font-size: 10pt;">P45985</a></div>

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<p style="orphans: 3; widows: 3; line-height: 1.5em; margin: 0.4em 0px 0.5em; color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; background-color: rgb(255, 255, 255);"><span id="parentSpecies:viewSpeciesDescription">Calcium Ion</span></p><div style="font-size: 12px; color: rgb(79, 79, 79); font-family: Arial, sans-serif; line-height: 14.390625px; background-color: rgb(255, 255, 255);">PubChem ID: <a name="cid2entrez" href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=271[uid]" style="outline: 0px; color: rgb(0, 153, 78); border: 0px; font-family: Arial, Verdana, sans-serif; font-size: 14px; line-height: 19px; vertical-align: baseline; margin: 0px; padding: 0px; text-decoration: none;">271</a></div>

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<font face="Arial, Verdana" size="2">mitogen-activated protein kinase</font><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase 1</span></div><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">UniProt ID: P28482</span></div><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);"><br/></span></div><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">Mitogen-activated protein kinase 3</span></div><div><span style="font-family: sans-serif; font-size: small; line-height: 16px; background-color: rgb(255, 255, 255);">UniProt Accession ID: P27361</span></div><div><br/></div><div>Extracellular signal-regulated kinases</div><div><span style="font-family: sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);"><br/></span></div>

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

<div><span style="line-height: 18.88888931274414px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Mitogen-activated protein kinase kinase 6 </font></span></div><font face="Georgia" size="2">UniProt ID: <a href="http://www.uniprot.org/uniprot/P52564" style="text-decoration: none; background-color: rgb(255, 255, 255);">P52564</a></font><div><font face="Georgia" size="2">Gene Name: <a href="http://www.ncbi.nlm.nih.gov/gene/5608" ref="ordinalpos=2&ncbi_uid=5608&link_uid=5608" style="line-height: 18.88888931274414px; white-space: nowrap; background-color: rgb(255, 255, 255);">MAP2K6</a></font></div><div><font face="Georgia" size="2">Gene ID: 5608</font></div>

2015-11-15T16:30:59Z

<div><font face="Georgia" size="2">The protein kinase c family consists of 15 isozymes in humans [49]. </font></div><div><font face="Georgia" size="2"><br/></font></div><div><font face="Georgia" size="2">Protein Kinase C alpha</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P17252">P17252</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCA</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5578</span></font></div><div><div><font face="Georgia" size="2">Protein Kinase C beta</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P05771" style="text-decoration: none; background-color: rgb(255, 255, 255);">P05771</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCB</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5579</span></font></div></div><div><div><div><font face="Georgia" size="2">Protein Kinase C gamma</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P05129" style="text-decoration: none; background-color: rgb(255, 255, 255);">P05129</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCG</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5582</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C delta</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q05655" style="text-decoration: none; background-color: rgb(255, 255, 255);">Q05655</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCD</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5580</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C epsilon</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q02156" style="text-decoration: none; background-color: rgb(255, 255, 255);">Q02156</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCE</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5581</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C eta</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P24723" style="text-decoration: none; background-color: rgb(255, 255, 255);">P24723</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCH</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5583</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C theta</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q04759" style="text-decoration: none; background-color: rgb(255, 255, 255);">Q04759</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCQ</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5588</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C iota</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/P41743" style="text-decoration: none; background-color: rgb(255, 255, 255);">P41743</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCI</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5584</span></font></div></div><div><div><font face="Georgia" size="2">Protein Kinase C zeta</font></div><div><font face="Georgia" size="2">Uniprot ID: <a href="http://www.uniprot.org/uniprot/Q05513">Q05513</a></font></div><div><font face="Georgia" size="2">Gene Name: PRKCZ</font></div><div><font face="Georgia" size="2">Gene ID:<span style="background-color: rgb(255, 255, 255); line-height: 16.78819465637207px; white-space: nowrap;">5590</span></font></div></div></div>

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

<font face="Georgia" size="2"><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">v-</span><span class="highlight" style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">src</span><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);"> avian sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog [</span><em style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">Homo sapiens</em><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">(human)]</span></font><div style="line-height: normal;"><font face="Georgia" size="2"><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">UniProt ID: </span><a href="http://www.uniprot.org/uniprot/P12931" style="text-decoration: none; background-color: rgb(255, 255, 255);">P12931</a></font></div><div><font face="Georgia" size="2"><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);">Gene Name: </span><a href="http://www.ncbi.nlm.nih.gov/gene/6714" ref="ordinalpos=1&ncbi_uid=6714&link_uid=6714" style="line-height: 17.999801635742188px; white-space: nowrap; background-color: rgb(255, 255, 255);"><span class="highlight">SRC</span></a></font></div><div><span style="line-height: 17.999801635742188px; background-color: rgb(255, 255, 255);"><font face="Georgia" size="2">Gene ID: 6714</font></span></div>

2015-11-15T16:30:59Z 2015-11-15T16:30:59Z 2015-11-15T16:30:59Z

Ras [2, 16, 14, 11] OR Rap1b [5, 8] OR PIP2_45 [6, 7] are positive regulators of Tiam, but are not sufficient. They are likely responsible for localizing Tiam to the membrane, so they are necessary but not sufficient and in an OR relation.\nOnce at the membrane, PH binding of PI3K products is necessary but not sufficient for Tiam activation [13, 16, 15, 1, 4, 6, 14]. Therefore PIP2_34 OR PIP3_345 are necessary but not sufficient.\nFinally, phosphorylation by either CamK [14, 12, 6, 7] OR Src [14, 12] OR PKC [14, 12] is necessary to turn on the GEF activity.\n\n

*Tiam binds to PIP3_345 {[13]-p(10)}\n<br>*Tiam binds to and is activated by PIP3_345 {[16]-p(7)}\n<br>*Tiam1 binds with high affinity to PIP2_34 and PIP3_345, but plasma membrane localization is independent of PI3K. {[15]-p(9)}\n<br>*PI3K can stimulate Rac activity through its product PIP3_345, which binds to Tiam, which is a GEF for Rac. {[1]-p(3)}\n<br>*In vitro, PIP3_345 directly and strongly activates the RacGEF activities of p-Rex1 and SSWAP-70, weakly those of Vav1, SOS1 and possibly Tiam1-controversial {[4]-p(2)}\n<br>*PIP3_345 can activate Tiam, but only after PIP2_45 has gotten it to the membrane. {[6]-p(864)}\n<br>*PIP2_45 and PIP3_345 bind to the same PH domain, so they compete. Therefore, their relative concentrations are important. {[6]-p(864)}\n

S_68 1 S_74 1 S_54 1 S_94 1 S_118 1 S_44 1 S_244 1 S_94 1 S_118 1 S_44 1 S_74 1 S_54 1 S_240 1 S_94 1 S_118 1 S_44 1 S_74 1 S_54 1

S_133 1 S_83 1 S_21 1 S_217 1 S_240 1 S_177 1 S_21 1 S_177 1 S_217 1 S_83 1 S_240 1 S_133 1

CaM is activated by Ca [2, 5, 3, 1].\n\n

*CaM is bound to {[2]-p(3), [5]-p(2)}\n<br>*Ca activates CaM {[3]-p(534)}\n<br>*If IP3 is not produced, then CaM is deactivated as well {[3]-p(534)}\n<br>*CaM is a signal mediator for Ca {[1]-p(1)}\n\n

S_229 1

Actin dynamics are very complicated and beyond the scope of this model. In this model Actin is only required for full focal adhesion formation. Therefore, Actin will be defined as ON when it is polymerized and bound to Myosin. Arp_2_3 OR IQGAP1 are (mainly) responsible for polymerization [31, 6, 2, 12, 19, 15, 17, 21, 3], so (Arp_2_3 OR IQGAP1) AND Myosin will activate Actin. However, when alpha_catenin is OFF (or in its homo-dimeric state - see [[alpha_catenin]] for OFF/ON definition) it will counteract the positive regulation of Arp_2_3 [13]. \n\n

*alpha_catenin binds to F-actin, competing off the binding with Arp2/3 {[13]-p.566}\n\n

*IQGAP1 binds to actin filaments {[3] -p(5)}\n<br>*IQGAP1 enhances actin polymerization {[21]-p.571, [21]-p.9}.\n<br>*Active Cdc42 enhances the binding of IQGAP1 to F-actin {[21]-p.572}.\n\n

*activated myosin causes increased contraction of actin {[24]-p(6), [23]-p(763), [8]-p(4)}\n\n

S_33 1 S_14 1 S_176 1 S_33 1 S_51 1 S_14 1

Gbg_s is an idealized Gbg that specifically binds Gas. Gbg_s is activated by the GPCR alpha-s_R when it is associated with Gas (i.e., when both Gas and Gbg_s are OFF). It is deactivated when Gas is GDP-bound (OFF) unless they are both OFF and B-AR is ON. If Gas is ON, then Gbg_s is separated and is ON. {[8, 1, 9, 6, 7, 3, 2] }\n\n

S_55 1 S_5 1 S_241 1 S_241 1

Gab1 is a negative regulator of Mekk3 [8, 6]. We will make it dominant. TNFR [8, 2, 4], Trafs [8, 7, 3], and Rac [8, 1] can all activate Mekk3 independently, so they are all in an OR. \n\n

*Gab1 regulates Mekk3. {[8]-p(662)}\n<br>*Gab1 is a negative regulator of MEKK3 {[6]-all}\n\n

*Rac can activate Mekk3 (through OSM). {[8]-p(662), [1]-all}\n\n

*Traf6 can activate Mekk3 (Il-1R activates Traf6) {[8]-p(662), [3]-all}\n<br>*Traf7 can activate Mekk3. {[8]-p(662), [7]-all}\n\n\n

S_160 1 S_154 1 S_61 1 S_154 1 S_123 1 S_154 1

The activator of Gaq is the GPCR alpha-q_R [14, 1, 4, 13, 12]. Gaq is activated by alpha-q_R when Gaq is OFF AND Gbg_q is OFF [1, 8, 11, 10, 5, 1, 12].\nGbg_q is a GDI for Gaq, which keeps Gaq OFF when it is OFF [8, 11, 10, 13].\nGaq is deactivated by RGS when Gaq is GTP-bound (i.e., ON) [9, 7, 2, 3, 13]. RGS is in an OR with PLCb [6, 3, 15]. We are requiring RGS OR PLC_B to stimulate the GTPase activity of Gaq, so if Gaq is ON and RGS OR PLCb is OFF, Gaq will stay ON even in the absence of alpha-q_R activation (unless there is an initial condition of Gbg_q OFF) otherwise, RGS and PLC_B would simply drop out of the logic. \n\n

*RGS functions as a GAP toward Ga subunits but not Gbg {[]-p(1), [7]-p(2)}\n<br>*RGS binds to Gaq to stop its activity {[2]-p(529)}\n<br>*RGS is a GAP for Ga {[]-p(1)}\n<br>*RGS interact most effectively with Gaq and block activation of PLCb. RGS4 activates Gaq's GTPase by 25 fold. {[15]-p(1301)}\n<br>*Many RGS proteins catalyze reapid GTP hydrolysis by isolated Ga subunits in vitro and attenuate agonist/GPCR_stimulated cellular responses in vivo {[13]-p(555)}\n<br>*Signalling is terminated by intristic GTPase activity og Ga and heterodimer reformation-a cycle accelerated by RGS {[13]-p(551)}\n\n

S_7 1 S_155 1 S_156 1 S_148 1 S_24 1 S_7 1 S_148 1

SEK1 [17, 23, 14, 26, 6, 21] OR MKK6 [4, 5, 17, 25, 22, 7, 21, 12, 26, 3, 11, 23, 6, 13, 8, 20, 14, 2, 27] OR MKK3 [5, 17, 25, 7, 6, 13, 12, 3, 11, 23, 8, 20, 14, 21, 26, 2] activate p38. PP2A [9, 11, 12] OR MKPs [24, 11, 19, 23, 20] are negative regulators of p38. They are made dominant.\n\n

*p38 is activated by MKK6 {[4]-p(342), [5]-p(3), Fig. 1, [17]-p(32), [25]-p(822), [22]-p(1), [7]-p(2-Fig. 1), [21]-p(1), [12]-p(1), [26]-p(322), [3]-p(665-Fig. 1)}\n<br>*p38 is activated and phosphorylated by MKK6 {[11]-p(1), [23]-p(66), [6]-p(3), [13]-p(2), [8]-p(2), [20]-p(187), Fig. 1}\n<br>*MKK6 is a dual specificity kinase that phosphorylates p38 {[14]-p(1)}\n<br>*Unlike MKK3, MKK6 is a common activator of all the isoforms of p38 {[14]-p(6)}\n<br>*MKK6 is specific for p38. {[2]-p(1)}\n<br>*Activation of p38 occurs through phosphorylation by MKK6 \nand MKK3 following exposure to cytokines. {[27]-p(2)}\n\n\n

*PP2A can dephosphorylate MEK1 and ERK-family kinases {[9]-p(3), [11]-p(2)}\n<br>*PP2A dephohphorylates p38 in vitro. {[12]-p(1)}\n<br>*Interaction of PP2A with p38 is specific. {[12]-p(2)}\n<br>*PP2A directly regulates p38 activity. {[12]-p(3)}\n<br>*PP2A inhibits p38, in vitro. {[12]-p(3)}\n\n

*MKP terminates the activity of SAPK and p38 by their dephosphorylation {[24]-p(6)} \n<br>*MPK-1 inactivates p38. {[11]-p(2)}\n<br>*MKP-3 is Erk-specific. It cannot dephosphorylate p38 or SAPK {[19]-p(3)}\n<br>*MKPs 1, 2 and 4 inactivate Erk, p38, and SAPK {[23]-p(76, 78)}\n<br>*MKP-5 both binds to and efficiently dephosphorylates p38 {[20]-p(188)}\n\n

*p38 is activated by MKK3 {[5]-p(3), Fig. 1, [17]-p(32), [25]-p(822), [7]-p(2-Fig. 1), [6]-p(3), [13]-p(2), [12]-p(1), [3]-p(665-Fig. 1)}\n<br>*p38 is activated and phosphorylated by MKK3 {[11]-p(1), [23]-p(66), [8]-p(2), [20]-p(187), Fig. 1}\n<br>*MKK3 is a dual specificity kinase that phosphorylates p38 {[14]-p(1, 4)}\n<br>*MKK3 is specific for only p38 a,j,d {[21]-p(1)}\n<br>*MKK3 is specific for only p38 a,b {[26]-p(322)}\n<br>*MKK3 is specific for p38. {[2]-p(1)}\n\n

*Sek1 can weakly activate p38 in only 10% of the rate which it activates SAPK {[17]-p(32)}\n<br>*Sek1 phosphorylates p38 in vitro {[23]-p(67)}\n<br>*Mekk1 is a poor activator of p38, despite the recognition of p38 by Sek1 {[23]-p(68)}\n<br>*MKK4 can activate both p38 and JNK {[14], [26]-p(322)}\n<br>*MKK4 can phosphorylate and activate p38 {[14]-p(4)}\n<br>*MKK4, but not MKK7 can also activate p38, but its not clear whether it's phosiologically a relevent activator {[6]-p(3)}\n<br>*MKK4 only activates p38a {[21]-p(1)}\n

S_226 1 S_43 1 S_147 1 S_26 1 S_43 1 S_147 1 S_239 1 S_43 1 S_147 1

EGFR_Y845 (Tyr_845 site of EGFR) is phosphorylated (hence activated) by Src. The activation of this site by Src appears to be EGF_dependent, EGF_activated EGFR homodimer is also required to be on for EGFR_Y845 to be "activated" [1]. Y845 can also be activated in an EGF_independent manner by the Integrin-Cas-Src complex; therefore, for this mechanism, EGFR_Free will be required.\n\n

*Src phosphorylates EGFR on Y845 {[10]-p(1),[8, 2]}\n<br>*Src phosphorylates EGFR on Y891 and Y920 (in vitro, []), as well as Y845 and Y1101 ([1],<cite>Jorrison</cite>-p.39). Y845 is phosphorylated by Src in vitro and vivo ([],<cite>Jorrison</cite>-p.39)\n<br>*Src is activated in response to growth factors such as PDGF, which induces PDFGR autophosphorylation {[12]-p(4)}\n<br>*Src kinase activity is required for phosphorylation of other tyrosine residues {[11]-p(2)}\n<br>*Src phosphorylation of EGFR at Y845 is likely not the mechanism of EGFR transactivation [5].\n<br>*Transactivation of EGFR is Src-independent {[9]-p(3)}\n<br>*Src phosphorylates Y845, Y1068, Y1086, and Y1173 (but not Y1148) when in complex with p130Cas and Integrins [13] This activation of the site is independent of EGF -- hence unliganded EGFR\nis necessary for this activation. [13, 3]\n\n

*See above Src\n\n

*See Src\n

*See above Src\n\n

S_244 1 S_52 1 S_41 1 S_244 1 S_129 1 S_200 1

Dynamin is activated or recruited either by [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]], [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]], [[Endophilin/Epithelial|Endophilin]],[[PIP2_45]] or [[Grb2]].{[4, 10, 9, 6, 3, 5]}\n\n

*Grb2 stimulates dynamin GTPase activity.{[10]-(p.3795)}\n

*Receptor stimulation leads to recruitment of dynamin to CCPs.{[4]-(p.1185)}\n\n

*Endophilin has been found at clathrin-coated pits and has been proposed to function in late stages of clathrin-mediated endocytosis by recruiting dynamin.{[9]-p(495)}{[6]-(SI p.7)}\n<br>*Membrane curvature is formed by endophilin. {[5]-p(354)}\n<br>*Endophilin interacts with dynamin and amphiphysin.{[3]-(p.3)}\n\n

*PIP2_45 along with their association with cargo RTKs and polymerization of clathrin set the stage for assembly of dynamin.{[5]-(p.35b354)}\n<br>*Dynamin associate with the plasma membrane through interaction wtih PIP2_45.{[3]-(p.8)}\n<br>*GTPase activity of dynamin is regulated by Gbg and PIP2_45.{[1]-(p.5057)}\n<br>*Dynamin is activated by PIP2_45.{[4]-(p.1185)}\n<br>*GTPase activity of dynamin is activated by PIP2_45.{[10]-(p.3795)}\n\n

S_52 1 S_157 1 S_118 1 S_19 1 S_185 1

GAK (auxilin2) supports the uncoating of clathrin from CCVs{[3]}. GAK is activated by interaction with clathrin, AP2, dynamin.{[2, 6, 3]} and binds to PIP2_45. Therefore, GAK is ON when ([[EGFR_EGFR_EGF_CCP/Epithelial|EGFR_EGFR_EGF_CCP]] OR [[EGFR_EGFR_TGFa_CCP/Epithelial|EGFR_EGFR_TGFa_CCP]]) AND ([[Dynamin/Epithelial|Dynamin]]OR [[AP2/Epithelial|AP2]] OR [[Clathrin]] OR [[PIP2_45]]). Furthermore, when GAK AND (EGFR_EGFR_EGF_CCV OR EGFR_EGFR_TGFa_CCV) are ON, we make GAK ON. This ensures that GAK is still present to uncoat the vesicle once it pinches off from the membrane.\n\n

*It's been suggested that interactions with clathrin, AP2, dynamin or other proteins recruit auxilin.{[2]-p(10268)} \n<br>*GAK binds to clathrin, AP2 and dynamin.{[3]-p(641)} \n<br>*Dynamin recruits auxilin.{[6]-p(930)} \n\n

* \n<br>*During coat-assembly, GAK is recruited to CCP.{[2]-p(10266)} \n\n

*It's been suggested that interactions with clathrin, AP2, dynamin or other proteins recruit auxilin.{[2]-p(10268)} \n<br>*GAK binds to clathrin, AP2 and dynamin.{[3]-p(641)} \n\n

*Upon separation from the plasma membrane, endocytic vesicles undergo uncoating in a process mediated by auxilin and Hsc70.{[4]-p(351)}{[5]-p(31.8)} \n<br>*GAK supports the uncoating of clathrin from CCVs.{[3]-p(641)} \n\n

*when GAK AND (EGFR_EGFR_EGF_CCV OR EGFR_EGFR_TGFa_CCV) are ON, we make GAK ON. This ensures that GAK is still present to uncoat the vesicle once it pinches off from the membrane.\n

*when GAK AND (EGFR_EGFR_EGF_CCV OR EGFR_EGFR_TGFa_CCV) are ON, we make GAK ON. This ensures that GAK is still present to uncoat the vesicle once it pinches off from the membrane.\n\n

S_30 1 S_10 1 S_183 1 S_159 1 S_11 1 S_66 1 S_29 1 S_174 1 S_10 1 S_183 1 S_159 1

Default Content.\n\n

*ARNO (expressed in chromaffin cells) is a potential GEF for ARF6 and other ARFs {[17]-p(1,2)}\n<br>*ARNO is a Arf1 GEF [13]\n\n

*PIP2_45 enhances activation of PLD and Arf activation by Arf GEF {[9]-p(251)}\n<br>*PIP2_45 regulates Arf-1 {[7]-p(768), Fig. 2}\n<br>*PIP2 like PIP3 may itself activate ARF proteins by recruiting the ARF exchange factors {[11]-p(3), [6]-p(3)}\n<br>*ArfGAP is PIP2_45 dependent or PIP3_345 dependent {[5]-p(6)}\n<br>*PIP2 can effect the regulation of ARFGEFs as well as ARFGAPs {[3]-p(90)}\n<br>*Binding of PIP2_45 to Arf is required for any GAP activity towards Arf1 [13]\n\n

*PIP2 like PIP3 may itself activate ARF proteins by recruiting the ARF exchange factors {[11]-p(3)}\n<br>*GRP (ARF GEF) axhibits an affinity for PIP3_345 {[11]-p(1)}\n<br>*A PH domain-containing ArfGAP is specifically activated by PIP3_345. {[16]-p(1), [6]-p(3)}\n\n

S_32 1 S_118 1 S_74 1 S_118 1 S_12 1 S_118 1 S_118 1 S_32 1 S_74 1 S_12 1

ErbB2_Y1248 (Tyr_1248 site of ErbB2) is activated when ErbB2 dimerizes with [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] [1].\n\n

ErbB2_Y1248 (Tyr_1248 site of ErbB2) is activated upon receptor dimerization [1].\n

ErbB2_Y1023 (Tyr_1248 site of ErbB2) is activated upon receptor dimerization [1].\n\n

S_220 1 S_91 1 S_195 1

MLCP turns Myosin OFF if it was ON [12, 11, 8, 3, 5]. If Myosin is OFF, MLCP has no effect and either RhoK [9, 15, 12, 5, 3, 10, 1, 20, 7] OR (CaM [4, 5, 8, 14] AND MLCK [13, 9, 19, 11, 12, 18, 5, 17, 14]) OR ILK [2, 3, 8, 7] OR PAK [9, 7] can turn ON Myosin. The same OR combination will activate Myosin if Mysosin AND MLCP are OFF, but if Myosin is ON and MLCP is OFF, Myosin will remain ON regardless. \n\n

*MLCP can be inhibited to produce Ca2+ sensitization, as well as enhanced to produce Ca2+ desensitization. {[4]-p(1)}\n<br>*MLCP regulates Ca2+ sensitity of myosin phosphorylation. {[5]-p(1)}\n<br>*CaM AND MLCK can activate myosin {[14]-p(178, fig. 1)}\n\n

*ILK may phosphorylate myosin within the basic sequence in chicken gizzard {[2]-p(4)}\n<br>*ILK can phosphorylate myosin at MLCK sites. {[3]-p(1)}\n<br>*ILK can phosphorylate MLC and myosin phosphotase subunit {[8]-p(6)}\n<br>*ILK can activate myosin independent of Ca/CaM (or anything else). {[8]-p(54), [7]-p(227)}\n\n

*MLCP dephosphorylates myosin {[11]-p(1)}\n<br>*MLCP binds to phosphorylated myosin and dephosphorylates it. {[12]-p(463)} \n<br>*Myosin is phosphorylated, and MLCP activity is inactivated. {[12]-p(469)}\n\n

*MLCK phosphorylates myosin when it gets activated by Erk {[13]-p(6), [9]-p(761), [19]-p(234)}\n<br>*MLCK activates Myosin {[11]-p(1)}\n<br>*MLCK phosphorylates and activates myosin. {[12]-p(468), [18]-p(10)}\n<br>*Phosphorylation of myosin by Ca2+/Calmodulin-regulated MLCK and MLCP is reversible. {[5]-p(1)}\n<br>*A rise in Ca2+ leads to activation of MLCK, followed immediately by a decrease in MLCP activity, which increases Ca2+ sensitivity. {[5]-p(1)}\n<br>*v-Src-induced Erk/MAPK activity stimulates MLCK activation and phosphorylation of myosin, which is presumed to induce actin-myosin contraction. {[17]-p(6)}\n\n

*RhoK phosphorylates myosin light chain and myosin phosphotase {[15]-p(246), [9]-p(762)}\n<br>*RhoK has been shown to enhance activity of myosin by inhibiting MLCP and by direct phosphorylation of MLC {[9]-p(763)}\n<br>*RhoK phosphorylates myosin and its subunit MBS, the latter of which leads to inactivation of MLCP. RhoK and MBS are believed to regulate myosin phosphorylation cooperatively. {[12]-p(463)}\n<br>*Activated RhoK phosphorylates myosin, thereby, inactivating MLCP {[12]-p(469)}\n<br>*Concomitantly,RhoK phosphorylates myosin at the same site that myosin is phosphorylated by MLCK and activates myosin. Both events are necessary for an increase in myosin phosphorylation. {[12]-p(469)}\n<br>*RhoK appears to regulate myosin phosphorylation downstream of Rho. {[12]-p(469, 474, 478)}\n<br>*RhoK phosphorylates myosin. {[5]-p(1), [3]-p(3), [10]-p(275), [1]-p(221)}\n<br>*RhoK can take the place of MLCK and phosphorylate myosin directly and thereby enhance its activity {[20]-p(3)}\n<br>*RhoK phosphorylates MLC at Ser19 and activates myosin ATPase activity, independently of Ca {[7]-p(221, 227)}\n\n

S_3 1 S_173 1 S_14 1 S_2 1 S_14 1 S_83 1 S_14 1 S_2 1 S_2 1 S_14 1 S_217 1 S_2 1 S_14 1 S_2 1 S_14 1 S_21 1 S_14 1 S_2 1 S_2 1 S_14 1 S_14 1 S_2 1 S_2 1 S_14 1 S_173 1 S_2 1 S_3 1 S_2 1 S_14 1

ESCRT_I is activated by ESCRT_0.\n\n

*Hrs (ESCRT_0) mediates the recruitment of ESCRT_I to endosomal membranes by binding to TSG101 in the ESCRT-1 complex.{[4]-p(644)} \n<br>*ESCRT_0 facilitates membrane recruitment of ESCRT_I.{[]-p(689)}\n<br>*ESCRT_0 recruits ESCRT_I to endosomes through direct interaction with Tsg101 (a component of ESCRT_0){[5]-p(553)}\n\n\n\n

S_215 1

This node represents the homodimer of EGFR activated by EGF during the endosome maturation, which involves fusion of early endosomes and creation of multivesicular bodies. Fast recycling of early endosomes appears to be inhibited by [[PKC/Epithelial|PKC]] and [[Cortactin/Epithelial|Cortactin]], and EGFR which did not go through fast recycling goes into MVB. During the endosome maturation, internalized EGFRs are sorted into different cellular destination. EGFR can be either recycled back in active form to the cell surface (slow recycling) or incorporated into the interlumenal membranes of MVB (i.e., maturing into late endosomes before fusing with lysosomes). EGFR_EGFR_EGF_MVB is activated by ([[EGFR_EGFR_EGF_End/Epithelial|EGFR_EGFR_EGF_End]] AND [[PKC/Epithelial|PKC]] AND [[Cortactin/Epithelial|Cortactin]]). EGFR_EGFR_EGF_MVB is inhibited when i) a slow recycling occurs, that is [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] is activated or ii) [[EGFR_EGFR_EGF_Lysosome/Epithelial|EGFR_EGFR_EGF_Lysosome]] is activated. Both of these inhibitors, however, only inactivate [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (i.e., when [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_SR]] was already on). Since receptor downregulation is considered as a default for EGF_induced receptor internalization (and in this version of the model we don't have all regulators of slow recycling), positive regulators are dominant over EGFR_EGFR_EGF_SR.\n\n

*Activaton of EGFR_EGFR_EGF_EGF_Lysosome results in removing (i.e., turns off) EGFR_EGFR_EGF_MVB . \n\n

*EGFR_EGFR_EGF_MVB is activated by EGFR_EGFR_EGF_End, which represents dymerized and activated EGFR in an early endosome.\n\n

S_16 1 S_72 1 S_227 1

PI3K [22, 26, 25, 30, 29, 15, 17, 32, 13, 4, 24, 11] OR PI5K [25, 10, 5, 6, 31, 7, 24, 8, 9, 3, 21, 14, 19] negatively regulate PIP4 by phosphorylation. PI4K [18, 25, 26, 10, 21, 14, 1, 19] OR (PTEN AND PIP2_34) [12, 29, 23, 20, 16, 24, 1, 16] are positive regulators of PIP4. The positive regulators are dominant to the negative ones when PIP4 is ON . Thus the negative regulators are dominant to the positive ones when PIP4 is OFF. \n\n

*In vitro PI3K phosphorylates PIP4 {[25]-p(486)}\n<br>*PI4Ks convert PtdIns to PIP4 thus generated can be further phosphorylated by both PI3K nad PI5Ks to yield PIP3_345 or PIP2_45,respectively.{[25]-p(492)}\n<br>*PI3K phosphorylates PIP4 and PIP2_45 producing PIP2_34 and PIP3_345 {[22]-p(1)}\n<br>*PIP4 is phosphorylated by class II of PI3k to generate PIP2_34 {[26]-p(764), Fig. 1}\n<br>*PI3K generates PIP2_34 and PIP3_345 {[15]-p(1), [17]-p(2), [32]-p(2905), [13]-p(193), [4]-p(211), [24]-p(968), Fig. 1, [11]-p(1)}\n<br>*PI3K phosphorylates PtdIns-4-P at the position 3 to synthesize PIP2_34. In addition, it can be synthesized by phosphorylation of PIP3 by PI4K {[25]-p(501, 502)}\n<br>*Activation of PI3K leads to generation of PIP2_34 and PIP3_345 {[30]-p(2)}\n<br>*Class II of PI3ks phosphorylate PIP4 to generate PIP2_345 {[26]-p(764), Fig. 1}\n<br>*PI3Ks phosphorylate 3'-OH position of PIP3,PIP2_34,PIP2_35 and PIP3_345 {[29]-p(1)}\n<br>*PI3K phosphorylates PIP4 and PIP2_45 producing PIP2_34 and PIP3_345 {[22]-p(1)}\n\n

* \n<br>*PTEN converts PIP2_34 to PIP_4 {[24]-Fig. 1, [1]-p(2)}\n<br>*PTEN (3'-phosphatase) converts PIP2_34 to PIP_4 and PIP3_345 to PIP2_45 {[29]-p(1), [1]-p(2), [16]-p(3)}\n<br>*PTEN dephosphorylates PIP2_34 and PIP3_345 at position 3 {[12]-p(1), [23]-p(4)}\n<br>*PTEN catalyzes dephosphorylation of PIP3_345 and PIP2_34 at the D position {[20]-p(1)}\n

*PI4Ks convert PtdIns to PIP4 thus generated can be further phosphorylated by both PI3K nad PI5Ks to yield PIP2_34 or PIP2_45,respectively. {[25]-p(492), [2]-p(7)}\n<br>*In the presence of PIP4, the PIP4K produces PIP2_45 {[25]-p(499)}\n<br>*PI is a substrate for PI4k, generating PIP_4 {[26]-p(762), Fig. 1}\n<br>*PI4K produces PIP_4 {[27]-p(16919), [28]-p(1)}\n<br>*PIP4 is generated by PI4Kb which is highly expressed in cardiomyocytes {[1]-p(1)}\n<br>*PI4K starts formation of PIP2_45 {[18]-p(2)}\n<br>*PI4Ks convert PtdIns to PIP4 thus generated can be further phosphorylated by both PI3K nad PI5Ks to yield PIP2_34 or PIP2_45,respectively. {[25]-p(492), [2]-p(7), [19]-p(88)}\n<br>*PIP_4 servers as a substrate for PIP_4 5-kinase ot yield PIP2_45 {[26]-p(762, 767), Fig. 1, [10]-p(3)}\n<br>*PIP2_45 is generated from PIP_4 by PIUP5K {[24]-Fig. 1}\n<br>*PIP_4 can be phosphorylated by PI5K to generated PIP2_45 {[21]-p(16919)}\n<br>*PIP5K typeI catalyses PIP4 to the formation of PIP2_45 {[14]-p(7840)}\n<br>*PIP2_45 can be synthesized either from phosphorylation of PIP4 by PI5K or through phosphorylation of PIP5 by PI4K {[1]-p(1)}. However, it is primarily generated through the first patwhay. PIP5 is a minor membrane constituent compared with PIP4 and PI5K is highly expressed in heart (Problem?!?){[1]-p(1)}\n<br>*In the presence of PIP4, the PIP4K produces PIP2_45 {[25]-p(499)}\n<br>*PI4K produces PIP_4 {[27]-p(16919), [28]-p(1)}\n<br>*PIP4 is generated by PI4Kb which is highly expressed in cardiomyocytes {[1]-p(1)}\n<br>*PI5K phosphorylates PtdIns-4-P at the position 5 to synthesize PIP2_45 OR PI4K phosphorylates PtdIns-5-P at the position 4 to synthesize PIP2_45 {[25]-p(501), [10]-p(3)}\n\n

*In vitro PIP4 is a substrate of PI5K {[25]-p(487-table 1)}\n<br>*PI4Ks convert PtdIns to PIP4 thus generated can be further phosphorylated by both PI3K nad PIP5Ks to yield PIP2_34 or PIP2_45,respectively. {[25]-p(492, 498)}\n<br>*PI5K phosphorylates PtdIns-4-P at the position 5 to synthesize PIP2_45 or PI4K phosphorylates PtdIns-5-P at the position 4 to synthesize PIP2_45 {[25]-p(501), [10]-p(2)}\n<br>*PIP5K type I phosphorates PIP_4 at D-% position of the inositol ring, commits the final step in PIP2_45 synthesis in vivo {[14]-p(7840)}\n<br>*PI5K catalyzes the synthesis of PIP2_45 {[5]-p.3(3585)}\n<br>*PI5K is responsible for synthesis of PIP2 {[6]-p(2), [31]-p(4)}\n<br>*PI5K produces pip2_45 {[7]-p(4), [24]-Fig. 1, [8]-p(96), Fig. 1}\n<br>*PLD stimulates further synthesis of PIP2_45 via PA stimulation of PI5K {[9]}-p(245) \n<br>*Rho directly effects PI5K, which in turn produces, PIP2_45. {[3]-p(2)}\n<br>*PIP_4 can be phosphorylated by PI5K to generated PIP2_45 {[21]-p(16919), [19]-p(88)}\n<br>*PIP5K type I phosphorates PIP_4 at D-5 position of the inositol ring, commits the final step in PIP2_45 synthesis in vivo {[14]-p(7840)}\n<br>*PI5K phosphorylates PtdIns-4-P at the position 5 to synthesize PIP2_45 OR PI4K phosphorylates PtdIns-5-P at the position 4 to synthesize PIP2_45 {[25]-p(501), [10]-p(3)}\n\n

S_196 1 S_54 1 S_17 1 S_106 1 S_17 1 S_219 1 S_17 1 S_208 1 S_17 1 S_106 1 S_17 1 S_219 1 S_17 1 S_17 1 S_106 1 S_219 1 S_106 1 S_17 1 S_219 1 S_17 1

Everything that makes IP3 will also make DAG, so either PLC_g or PLC_B can hydrolyze PIP2_45 to IP3; both are AND to PIP2_45 [21, 28, 3, 25, 6, 16, 34, 30, 19, 35, 7, 17, 26, 14, 2, 31, 12, 1, 32, 5, 20]\nDGK is a negative regulator that inactivates DAG [23, 4, 8, 10, 11].\nAlthough, another way to creat DAG exist through the conversion from PA, DAG synthesized from PA is monoDAG which does not seem to regulate the same effectors as polyDAG which is synthesized from PIP2_45. [8, 11, 10] Therfore, PA is not an input to DAG.\nThus, the PA and PLC/PIP2_45 pathways are the two major ways to get DAG. They are OR if DAG is OFF (because DGK falls out if DAG is OFF), but the PA/DAG/DGK pathway (which is negative) is dominant if DAG is ON.\n\n

*DAG is generated by PLC {[16]-p.2(282), [29]-p(142)}\n<br>*DAG is generated by PLCb {[2]-p(2, Fig.1)}\n<br>*PLCb produces IP3 and DAG {[20]}-p(1638)}\n<br>*The cleavage of PIP2_45 by PLC_generates DAG and IP3 {[24]-p(968)}\n<br>*DAG and IP3 are generated by PLC from PIP2_45 {[19]-p(1239), [35]-p(236)}\n<br>*DAG and Ca2+ are generated by PLCg {[18]-p(380), Fig. 5}\n

*DAG is downstream of PIP2 {[30]-p(5, Fig.3)}\n<br>*PIP2_45 is cleaved into IP3 and DAG by PLCg when activated by EGFR {[7]-p(1)} \n<br>*DAG is generated by PLC or PLD from PIP2_45 [34]\n<br>*DAG is generated after PLC hydrolyzes PIP2_45 {[21]-p(1), [28]-p(1), [3]-p(260), [25]-p(1), [12]-p(232), [6]-p(1), [17]-p(340), [33]-p.889}\n<br>*PIP2_45 is a precursor for DAG {[16]-p.2(282), [26]-p(502), [5]-p(1)}\n<br>*hydrolysis of PIP2 produces DAG {[2]-p(3, Fig.2), [31]-p(1), []-p(4), [1]-p(6)}\n<br>*PIP2_45 is hydrolyzed by phospholipses to generate IP3_145 and DAG {[27]-p(762, 765, 766), [32]-p(3)}\n<br>*The cleavage of PIP2_45 by PLC_generates DAG and IP3 {[24]-p(968)}\n<br>*DAG and IP3 are generated by PLC from PIP2_45 {[19]-p(1239), [35]-p(236)}\n\n

S_18 1 S_39 1 S_155 1 S_118 1 S_39 1 S_18 1 S_175 1 S_118 1 S_39 1 S_18 1

Shc OR EGFR_Y1068 OR EGFR_Y1086 OR ErbB2_1139 can activate Grb2. In an OR with the aforementioned regulators is Fak AND Src. Fak and Src are AND because after Fak is activated by integrins, Src must phosphorylate the sites of Fak that activate Grb2 [3, 11, 23, 15]. \n\n

*Figure 1 suggests that Grb2 may be regulated by Shc {[34]-p(3,Fig.1)}\n<br>*Grb2 can bind EGFR directly or through Shc {[29]-p(1,2)}\n<br>*SOS/Grb2 complex is bound to Shc {[4]-p(7), [31]-p(1)}\n<br>*GPCR activation induces a rapid increase in tyrosine phosphorylation of Shc and Grb2 association {[32]-p(1)}\n<br>*Shc can bind Grb2 {[5]-p(2),[19]-p(2,Fig.1),[27]-p(2)}\n<br>*Grb2 binds directly to Shc through its SH2 domain {[9]-p(2),[16]-p(3)}\n<br>*Shc can recruit Grb2 proteins thereby potentiating the signals by the activates receptor {[28]-p(2)}\n<br>*The dephosphorylation of Shc by PTEN inhibited the recruitment of Grb2, which leads to downregulation of MAP kinases. {[33]-p(36)}\n<br>*She becomes phosphorylated on tyrosine residues, creaign additional docking sites for Grb2. {[25]-p(3)}\n\n

*FAK creates a binding site for the SH2 domain of Grb2 and presents one mechanism of activation of hte Ras/Erk pathway by FAK {[13]-p(2, 12)}\n<br>*FAK can bind Grb2 {[5]-p(2)}\n<br>*Grb2 directly binds to FAK {[14]-p(441, 457), Fig. 3, [18]-p(1)}\n<br>*Grb2 is recruited by FAK {[8]-p(1)}\n<br>*Phosphorylated Fak interacts with Grb2, leading to MAPK activation {[31]-p(1), [23]-p(1411)}\n<br>*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[3]-p.2(3584), [11]-p(59), [23]-p(1410)}\n

S_136 1 S_127 1 S_78 1 S_73 1 S_244 1 S_135 1

This node represents the ErbB3:ErbB4 heterodimer. It is activated by ErbB3_Free (representation of an inactive ErbB3) AND ErbB4_Free (representation of an inactive ErbB4) AND NRG. Due to the hierarchy in the activation of the various ErbB's, the activation of ErbB3_ErbB4 occurs only when ErbB2_Free is not present.\n\n

*Neurogulins promote ErbB3:ErbB4 heterdimers [] \n\n

*ErbB2 is the preferred dimerizing partner for all ErbBs [] ; Hence ErbB2_Free will be a negative regulator of other dimers.\n

*ErbB3_ErbB4 is activated by ErbB4_Free, which represents unliganded ErbB4 on the cell surface.\n\n

*EGFR_ErbB3 is activated by ErbB3_Free, which represents inactive ErbB3 on the cell surface.\n\n

S_107 1 S_125 1 S_31 1 S_117 1

PKA is a dominant negative regulator of PAK [3, 7, 27, 9, 14, 42].\nAkt is a negative regulator dominant to Nck [27, 41].\nPTP1b is a negative regulator dominant to Src [19].\nCdc42 [35, 31, 28, 27, 32, 16, 36, 18, 22, 20, 4, 30, 37, 13, 10, 2, 15, 38, 34, 8, 17, 6] OR Rac [35, 31, 4, 27, 16, 36, 18, 30, 37, 13, 32, 11, 10, 22, 2, 38, 34, 8, 33, 1] can activate PAK when PAK is bound to Nck [34, 27, 16, 36, 18, 23, 24] OR Grb2 [27]. PAK also seems to be a PDK1 substrate [39, 27], however the PDK1 on PAK activation seems to be T cell and PDGF dependent. [27] Therefore, for now, PDK1 is included in the table, but has no effect. \nSrc phosphorylates PAK to enhance its activity when its already ON due to Cdc42/Rac activation, therefore it will keep PAK ON if PAK AND (Cdc42 OR Rac) is ON [19, 27].\n\n

*Akt phosphorylates PAK1 at Ser21 , and this decreases binding of Nck to the PAK1 N-terminus and stimulates PAK1 activity in GTPase-independent manner in vivo {[27]-p(752)}\n<br>*one of Akt/PKB is the phosphorylation and activation of PAKa {[41]-p(3475)}\n\n\n

*PAKs can interact with Nck and Grb2 via their domains to recruit Paks to activated TKRs at the plasma membrane {[27]-p(751)}\n\n

*The Paks have been proposed to transduce signals from Cdc42 and Rac to the SAPK and p38 pathway {[35]-p(5)}\n<br>*Paks are activated by Cdc42 and Rac {[31]-p(3), [4]-p(4), [27]-p(749), [16]-p(5), [36]-p(1), [18]-p(3)}\n<br>*Paks are activated by Rac {[30]-p(2-Fig. 1), [36]-p(1)}\n<br>*Pak is a Cdc42 and Rac target {[30]-p(3). [37]-p(170), [13]-p(4), [27]-p(744), [32]-p(466), [11]-p(2), [10]-p(418), [22]-p(1), [2]-p(165)}\n<br>*all mammalian PAKS bind Rac1 and Cdc42Hs and the binding is necessary for activtion of PAK {[38]-p(34)}\n<br>*PAK activity and autophosphorylation are stimulated by Rac-GTP or Cdc42-GTP {[34]-p(91)}\n<br>*PAK is stimulated by Rac. {[8]-p(2)}\n<br>*Attachment to extracellular matrix enhances the ability of activated Rac to stimulate PAK {[36]-p(1)}\n<br>*Rac binds and activates PAK {[33]-p(292, 299), Fig. 3}\n<br>*Rac1-GTP can activate PAK1 {[1]-p(2326)}\n\n

*PTP1b dephosphorylates PAK and counteracts the action of Src phosphorylation {[]}\n

*PKA phosphorylates (inhibits) PAK {[3]-p(4), [7]-p(2)}\n<br>*PKA interacts with PAKs {[27]-p(752)}\n<br>*PKA activity is suppressed upon adhesion and elevated in detached cells where it accelerates the dephosphorylation of FAK and inactivation of PAK1, effects that can be reversed by expressing activated PAK1. {[9]-p(1)}\n<br>*PKA has been shown to phosphorylate and inhibit VASP and PAK and to activate RAc1 and Cdc42 {[14]-p(577)}\n<br>*PAK is inhibited by PKA which antagonizes PAK interaction with PIX and also phosphorylation of MLCK. {[42]-p(2)}\n\n

*PAKs 1 and 3 bind to Nck {[34]-p(71)}\n<br>*PAKs can interact with Nck and Grb2 via their domains to recruit Paks to activated TKRs at the plasma membrane {[27]-p(751)}\n<br>*Nck targets Pak to the membrane {[16]-p(5)}\n<br>*Activated PDGFR recruits Pak1 to the cell membrane by Nck's binding to the PDGFR {[16]-p(7)}\n<br>*Nck mediates interaction of PAK with the membrane. {[36]-p(1)}\n<br>*Nck mediates PAK association with the PDGF receptor, an important event required for PAK activation. {[18]-p(3)}\n<br>*Nck recruits PAK to the RTKs {[23]-p(6)}\n<br>*PAK recruitment by Nck to EGFR leads to its rapid activation {[24]-p(2)}\n\n

*The Paks have been proposed to transduce signals from Cdc42 and Rac to the SAPK and p38 pathway {[35]-(5)}\n<br>*Paks are activated by Cdc42 and Rac {[31]-p(3), [28]-p(828), [27]-p(749), [32]-p(466), [16]-p(5), [36]-p(1), [18]-p(3), [22]-p(1)}\n<br>*Pak is activated by Cdc42 {[20]-p(2-Fig. 1), [4]-p(4)}\n<br>*Pak is a Cdc42 and Rac target {[30]-p(3), [37]-p(170), [13]-p(4), [27]-p(744), [10]-p(418), [2]-p(165)}\n<br>*Pak is a Cdc42 target. {[15]-p(1)}\n<br>*Pak is a downstream effector of Cdc42 {[40]-p(1)}\n<br>*all mammalian PAKS bind Rac1 and Cdc42Hs and the binding is necessary for activtion of PAK {[38]-p(34)}\n<br>*PAK activity and autophosphorylation are stimulated by Rac-GTP or Cdc42-GTP {[34]-p(91)}\n<br>*PAK is stimulated by Cdc42. {[8]-p(2)}\n<br>*Activation of PKA by Fsk can promote phosphorylation and inhibition of PAK1. {[2]-p(165)}\n<br>*GTP-bound Cdc42 can efficiently activate the high local concentration of PAK {[17]-p(173)}\n<br>*PAKs can bind to and be activated by CDC42 and RAC {[6]-p(878)}\n\n

S_132 1 S_85 1 S_103 1 S_19 1 S_133 1 S_160 1 S_19 1 S_85 1 S_103 1 S_133 1 S_244 1 S_21 1 S_160 1 S_132 1 S_79 1 S_133 1

We are modeling GRK mostly after GRK2. Erk negatively regulates GRK {[8]}. It will be made dominant. RKIP is also a negative regulator to inhibit GRK2 {[7, 4]}\n{Gbg_s OR Gbg_i OR Gbg_q OR Gbg_12_13} AND PIP2_45 positively regulate GRK {[2, 3]}\nB_Arrestin AND Src are positive regulators {[8, 9]}. PKC only enhances, so it is included as an input, but it drops out of the logic {[3]}.\n\n

*GRK2 is phosphorylated by Src which required Src to be in complex with barrestin {[8]-p(7972)}\n\n

*Phosphorylation of GRK2 by ERK decreases GRK2 translocation to the membrane and markedly reduces GRK2 kinase activity {[8]-p(7972)}\n

*PIP2_45 binds to the amino terminus if a GRK PH domain lacking the carboxyl-terminal sequences required for Gbg binding {[3]-p(663)}\n<br>*PIP2_45 doesn't directly activate GRK2 {[3]-p(666)}\n\n

*RKIP switches between GRK2 and Raf-1; Inhibits them. {[1], [5], [7], <cite>Lorenz</cite>}\n<br>*RKIP is specific for GRK2 {[7]-p(92)}\n<br>*RKIP binds GRK2 {<cite>Trakul</cite>-p(24931)}\n\n

S_89 1 S_118 1 S_191 1 S_234 1 S_148 1 S_118 1 S_191 1 S_234 1 S_222 1 S_118 1 S_191 1 S_234 1 S_5 1 S_118 1 S_191 1 S_234 1 S_95 1 S_244 1 S_191 1 S_234 1

alpha-q_R is stimulated by its ligand alpha-q_lig. GRK phosphorylates alpha-q_R, but this has no effect on its own [10, 6, 4, 9, 8]. When GRK does phosphorylate alpha-q_R, B_Arrestin has to be ON to turn alpha-q_R OFF [5, 1]. GRK only phosphorylates alpha-q_R when alpha-q_R is ON [6], so alpha-q_R will be an input to itself.\nThe external inputs will not be dominant to the negative regulators (otherwise the negative regulators really have no effect). \nNote, our GPCRs are separated into two nodes so that more realistic and precise simulation can be conducted. Since the phosphorylation of GPCRs and the sequestering by B_Arrestin are two seperate events, we have a phosphorylated version of each GPCR. This phosphorylated GPCR (Palpha-q_R,Palpha-12_13_R, etc.) has its own logic table and acts as a node on its own during the simulations.\n\n

*B-arrestin down-regulates GPCR by interrupting the interaction between the receptor and the G-prot. {[5]-p(1534); [7]-all}\n<br>*Membrane recycling can turn off GPRC {[5]-p(1534)}\n<br>*b-arresins desensitizes 7MSRs by structurally blocking their interaction with G-prot. {[1]-p(1), [7]-all}\n<br>*b-arrestins uncouple the receptor from the G prot. and may target many GPCRs for internalization in specialized membrane areas {[2]-p(1940)}\n\n

S_45 1 S_95 1 S_231 1 S_45 1 S_231 1 S_24 1 S_24 1 S_95 1 S_231 1 S_45 1 S_231 1 S_24 1 S_231 1 S_95 1 S_95 1 S_231 1 S_45 1 S_231 1 S_24 1

[[Rabaptin_5/Epithelial|Rabaptin_5]] brings Rabex_5 close to Rab5_GDP on the early endosome.{[1]-p(4)} \n\n

*Rabaptin_5, which is a Rab5 effector brings Rabex_5 to the proximity of Rab5-GDP on the early endosome. This may lead to further Rab5 activation in a positive feedback loop.{[1]-p(4)} \n\n

S_70 1

TAO_1_2 [12] OR Tpl2 [11, 5] OR TAK1 [6, 9, 3, 11, 2] OR MLK3 [9, 2, 11] OR MLK2 [11] OR MLK1 [11] OR MEKK4 [11, 5, 2] OR MEKK3 [8, 3, 11, 5, 14, 7] OR MEKK2 [11, 5] OR PAK [9, 5] can activate MKK3. ASK1 also activate MKK3 [6, 11, 9, 7, 3, 1, 13, 4, 5] and since ASK1 is required for p38/SAPK activation, ASK1 will be in an AND with the other activators. \n\n\n

*MKK3 is activated by ASK1 {[6]-p(3), Fig. 1, [11]-p(822), [9]-p(2-Fig.1), [7]-p(69)}\n<br>*ASK1 can activate MKK3 {[3]-p(33), [1]-p(1059)}\n<br>*ASK1 phosphorylates and activateds MKK4 or MKK7 and MKK3 or MKK6 {[13]-p(893, 897), [4]-p(1), [5]--p(187), Fig. 1}\n<br>*ASK1 is necessary for the sustained activation of p38/SAPK, so it is likely necessary for Sek1 activation. {[10]-p(263)}\n\n

*MEKK2 can activate MKK3 {[11]-p(822), [5]-p(187), Fig. 1}\n\n

*Pak is displayed as an activator of MKK3 and MKK6 {[9]-p(2-Fig. 1), [5]-p(187), Fig. 1} \n\n

*MKK3 is activated by MLK3 {[9]-p(2-Fig. 1), [2]-p(6)}\n<br>*MEKK4 or TAK1 or MLK3 appear to activate MKK3 {[2]-p(4)}\n<br>*MLKs activate MKK3. {[11]-p(822)}\n\n

*MEKK4 can activate MKK3 {[11]-p(822), [5]-p(187), Fig. 1}\n<br>*MEKK4 or TAK1 or MLK3 appear to activate MKK3 {[2]-p(4)}\n\n

*TAO_1_2 can activate MKK3. {[12]-all}\n\n

*MKK3 is activated by TAK {[6]-p(3-Fig. 1), [9]-p(2-Fig. 1)}\n<br>*TAK can activate MKK3 {[3]-p(33), [11]-p(822), [2]-p(5)}\n<br>*MEKK4 or TAK1 or MLK3 appear to activate MKK3 {[2]-p(4)}\n\n

*MEKK3 can phosphorylate and activate MKK3 in vitro, but no activation of p38 enduces when MEKK3 is expressed in vivo w/ w/out MKK3 {[8]-p(4)}\n<br>*MEKK3 can activate MKK3 {[3]-p(33), [11]-p(822), [5]-p(187), Fig. 1, [14]-p(662)}\n<br>*Mekk3,in vitro, phosphorylates Mek,Sek1 and MKK3 {[7]-p(68)}\n\n

S_49 1 S_236 1 S_221 1 S_236 1 S_42 1 S_236 1 S_204 1 S_236 1 S_97 1 S_236 1 S_21 1 S_236 1 S_150 1 S_236 1 S_216 1 S_236 1 S_146 1 S_236 1 S_6 1 S_236 1

EGFR_Y1101 (Tyr_1101 site of EGFR) is phosphorylated (hence activated) by Src.\n\n

*Src phosphorylates EGFR on Y891 and Y920 (in vitro, []), as well as Y845 and Y1101 ([2],<cite>Jorrison</cite>-p.39,[3]). Y845 is phosphorylated by Src in vitro and vivo ([],<cite>Jorrison</cite>-p.39)\n<br>*Src is activated in response to growth factors such as PDGF, which induces PDFGR autophosphorylation {[6]-p(4)} \n<br>*Src kinase activity is required for phosphorylation of other tyrosine residues {[5]-p(2)}\n\n

S_244 1

Trx will be called OFF when it is reduced and ON when it is oxidized. It is normally OFF (reduced) and is turned on by Stress (particularly oxidative stress) [1]\n\n

*Stress activate (oxidizes) Trx. It is normally OFF (reduced) {[1]-p(3, 7)}\n\n

S_123 1 S_86 1

This node represents EGF_activated homodimer of EGFR localized in clathrin-coated vesicles. CCPs are pinched off from the plasma membrane by a [[Dynamin/Epithelial|Dynamin]] and [[Actin]]-dependent mechanism {[6, 2]}. Since EGFR_EGFR_EGF_CCV inherits [[PIP2_45]], [[AP2/Epithelial|AP2]] and [[Clathrin]] from [[EGFR_EGFR_EGF_CCP/Epithelial|EGFR_EGFR_EGF_CCP]], EGFR_EGFR_EGF_CCV will be activated by (EGFR_EGFR_EGF_CCP AND Dynamin AND Actin AND PIP2_45 AND AP2 AND Clathrin OR GAK). Furthermore, once CCVs fuse with early endosomes, EGFR_EGFR_EGF_CCV will be replaced by [[EGFR_EGFR_EGF_End/Epithelial|EGFR_EGFR_EGF_End]], EGFR_EGFR_EGF_End acts as a negative regulator of EGFR_EGFR_EGF_CCV. Furthermore, when EGFR_EGFR_EGF_CCV is ON, it remains on until shut off by negative regulators. \n\n\n

*Activated EGFR is entrapped in clathrin-coated vesicles by a dynamin and actin-dependnet pinching off mechanism. {[6]-p(610)}{[2]-p(1531)}\n\n

*Activated EGFR is entrapped in clathrin-coated vesicles by a dynamin and actin-dependnet pinching off mechanism. {[6]-p(610)}{[2]-p(1531)}\n<br>*Dynamin is required to pinch off vesicles from the plasma membrane.{[5]-p(929)}\n\n

*EGFR_EGFR_EGF_CCV is activated by EGFR_EGFR_EGF_CCP, which represents dymerized and activated EGFR in a clathrin-coated pit.\n\n

*Activaton of EGFR_EGFR_EGF_End results in removing (i.e., turns off) EGFR_EGFR_EGF_CCV. \n\n

S_29 1 S_227 1 S_174 1 S_4 1 S_10 1 S_227 1

This node represents TGFa-activated homodimer of EGFR localized in clathrin-coated pits. Ubiquitinated EGFR is sorted into CCPs by binding to [[AP2/Epithelial|AP2]], [[Eps15/Epithelial|Eps15]] or [[Epsin/Epithelial|Epsin]].([6, 8, 11, 13, 7, 3]) Furthermore, activated [[Rab5/Epithelial|Rab5]] is important for sequestering ligands into CCPs, and [[PIP2_45]] and [[Clathrin/Epithelial|Clathrin]] are necessary for the invagination of CCP.{[, 4]} Therefore, EGFR_EGFR_TGFa_CCP is activated by (PIP2_45 AND Clathrin AND Rab5 AND (Eps15 OR Epsin OR AP2)). When CCPs are pinched off from the plasma membrane and CCVs are created, [[EGFR_EGFR_TGFa_CCV/Epithelial|EGFR_EGFR_TGFa_CCV]] will replace EGFR_EGFR_TGFa_CCP. Therefore, EGFR_EGFR_TGFa_CCV acts as a negative regulator of EGFR_EGFR_TGFa_CCP when it was previously on and made dominant to EGFR_EGFR_TGFa_CCP.\n\n

*PI(4,5)P2 is enriched in the plasma membrane and is required for the invagination of CCPs.{[4]-p(31.25)}\n

*Clathrin is assembed to form CCPs and cargo (EGFR) is recruited.{[5]-p(312)}\n\n

*Endocytosed receptors are sorted into CCPs by interaction with the clathrin-binding AP-2 complex or by binding to other adaptor proteins, which in turn interacts with the clathrin heavy chain and/or AP2.{[6]-p(610)}{[8]-p(565)}{[11]-p(12111)}{[13]-p(793)}{[7]-p(R49)} \n\n

*Activaton of EGFR_EGFR_TGFa_CCV results in removing (i.e., turns off) EGFR_EGFR_TGFa_CCP.\n\n

*Eps15 and epsin recruits(activates) EGFR to CCPs. {[6]-p(610)}{[]-p(171)} \n\n

*Activated Rab5 is important for sequestering ligands into CCPs and subsequent fusion of vesicles with early endosomes.{[12]-p(184)}{[1]-p(110)}\n\n

S_30 1 S_66 1 S_36 1 S_192 1 S_157 1 S_118 1 S_183 1 S_159 1 S_118 1 S_183 1 S_157 1 S_192 1 S_225 1 S_157 1 S_118 1 S_183 1 S_192 1

ErbB3_Free represents ligand-free, inactive ErbB3. The Off state of this node corresponds to non-existing ErbB3 on cell surface. On the other hand, the On state depicts the presence of ligand-free ErbB3, ready to be activated by any of its ligands. To simulate the model under different levels of ErbB3 expression, this node has an external node - ErbB3_Controller - which is responsible for providing the model with inactive ErbB3's (and hence activates ErbB3_Free).<BR>\nUpon binding to their ligand, ErbB3 dimerizes with other ErbB3's or other types of ErbB's. When dimerized, ErbB3 is removed from the pool of free, inactive ErbB3's, therefore the following nodes representing active ErbB3 dimers act as negative regulators of ErbB3_Free: [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]], and [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]]. ([6, 2, 5, 9, 4, 1])\n\n

ErbB2_ErbB3 dimerization results in removing (i.e., turns off) a ErbB3 from the ErbB3_Free pool.\n\n

EGFR_ErbB3 dimerization results in removing (i.e., turns off) a ErbB3 from the ErbB3_Free pool.\n

S_31 1 S_91 1 S_99 1 S_20 1 S_171 1

PIP2_45 activates ARNO [1]\n\n

*The GEF activity of ARNO is dependent on its binding to PIP2_45 {[1]-p.3}\n\n

S_118 1

Ca AND Calmodulin are negative regulators of IQGAP1 [2, 1]\n

S_3 1 S_229 1 S_3 1 S_229 1

This node represents the ErbB4:ErbB4 homodimer. It is activated by ErbB4_Free (representation of an inactive ErbB4) AND NRG. Due to the hierarchy in the activation of the various ErbB's, the activation of EGFR_ErbB2 occurs only when ErbB2_Free is not present.\n\n

*Neurogulins bind specifically to ErbB4 [] \n\n

*ErbB2 is the preferred dimerizing partner for all ErbBs []; Hence ErbB2_Free will be a negative regulator of other dimers.\n\n

EGFR_ErbB4 is activated by ErbB4_Free, which represents inactive ErbB3 on the cell surface.\n\n

S_107 1 S_125 1 S_117 1

S_233 1 S_203 1 S_237 1

*Epsin is recruited by activated EGFR.{[3, 4, 7]} Furthermore, ubiquitinated EGFR provides attachment sites for Epsin.{[5, 10, 7]}, and [[PIP2_45]] is essential for epsin localization. {[8, 1, 7]} Therefore, in our model, Epsin is activated either by [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] OR [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] OR [[EGFR_Ub/Epithelial|EGFR_Ub]] OR [[PIP2_45]] .\n\n

*Epsin binds to EGFR ubiquitinated by Cbl. {[5]-p.8-9}\n<br>*Ubiquitinylation of EGFR establishes multiple attachment sites for proteins containing an ubiquitin-binding domain like Eps15 and epsin{[7]-p.349}{[10]-p.417} \n\n

*Epsin is recruited by activated EGFR{[7]-p(349)}{[4]-p(567)}\n\n

*Epsin is recruited and activated by EGFR{[7]-p(349)}{[4]-p(567)}\n<br>*Epsin is phosphorylated and activated by EGFR {[3]-p(906)}\n\n

* On binding PIP2_45, epsin drives membrane curvature, thereby committing to clathrin-coated vesicle formation.{[11]-p(172)}{[7]-p(354)}{[8]-p(31.9)}\n<br>*Epsin binds to PIP2_45 and AP-2.{[1]-p(3,5)}\n

S_52 1 S_157 1 S_118 1 S_65 1

Rabenosyn_5 is a Rab5 effector, and the recruitment of Rabenosyn_5 require both Rab5 and PIP3_345.{[1]}\n\n

*The concomitant presence of Rab5 and PIP3 allows the recruitment of Rab5 effectors EEA1 and Rabenosyn_5.{[1]-p(111)}\n

*The concomitant presence of Rab5 and PIP3 allows the recruitment of Rab5 effectors EEA1 and Rabenosyn_5.{[1]-p(111)}\n\n

S_192 1 S_74 1

Cdc42 activates WASP [11, 4, 27, 23, 12, 6, 24, 21, 7, 26, 25, 17, 22, 13, 8, 9, 5] and Crk is in an AND with Cdc42 [14]. Ccd42 AND Crk are necessary, but they also require either the activity of Nck [14, 11, 7, 2] OR Grb2 [22, 20, 2], or the activity of PIP2_45 [11, 4, 21, 7, 26, 25, 24, 2, 23, 14, 9, 5]\nFinally, phophorylation by either Src OR Fak is required for WASP activity [10, 3, 10, 9].\nPTPPEST negatively regulates the phosphorylation of WASP, and there is evidence that it works against the phosphorylation of the Src family kinases [1, 16, 28].\n\n

*Src phosphorylates WASP (at the same site as Fak) which significantly enhances the ability of WASP to activate Arp23. {[9]-p.960}\n\n

*WASP is a substrate of PTPPEST {[1]-p(166)}\n<br>*There is eveidence that PTPPEST works against phosphorylation of WASP by Src family kinases. {[16]-all, [28]-all}\n\n

*N-WASP interacts with Grb2. {[22]-p(466)}\n<br>*Grb2, which is a weak activator by itself, cooperates with Cdc42 to elicit full WASP and N-WASP activity, in a similar way to the actions of NCK and PIP2_45. {[20]-p(3)}\n<br>*Nck and Grb2 activate N-WASP via binding to the proline-rich domain of N-WASP. {[2]-p(7)}\n\n

*FAK influences N-WASP by phosphorylating it; It only associates with an activated N-WASP, and doesn't itself activate WASP. However, its phosphorylation doesn't effect N-WASP activity towards Arp2/3, but it seems to be important for maintaining a cytoplasmic distribution of N-WASP and for promoting cell motility {[10]-p(63), [3]-p(9574,9575)} (Suggest disregard this connection due to no signalling effect)\n<br>*FAK phosphorylates Cdc42-activated N-WASP, thereby retaining phosphorylated N-WASP in the cytoplasm where it can affect ARP2/3-mediated actin polymerization {[10]-p(62)}\n<br>*Fak phosphorylates WASP which significantly enhances the ability of WASP to activate Arp23. {[9]-p.960}\n\n

*Crk and Paxillin complex is also required to activate N-WASP {[14]-p(23387)}\n<br>*Crk and Cdc42 are required for WASP activation, however Crk seems to act on Cdc42 through DOCK180 in order to help activate N-WASP{[14]-p(23387,88)}\n\n

*WASP gets activated by PIP2 and CDC42 {[11]-p(10),[4]-p(97)}\n<br>*WASP is activated by signaling molecules such as PIP2_45 and Cdc42 {[21]-p(8),[7]-p(578),[26]-p(175),[25]-p(128)}\n<br>*WASP possesses a PH domain that binds PIP2 {[24]-p.170,[2]-p(6)} \n<br>*PIP2 potentiates Cdc42 activation of WASP {[2]-p(7)}\n<br>*Small GTPase Rac acts in PIP2 to regulate ERM and WASP {[23]-p(768),[14]-p(23388)}\n<br>*Nck AND PIP2 activate WASP independently of Cdc42 {[14]-p(23388)}\n<br>*N-WASP's self-inhibition is relieved by the cooperative binding of active Cdc42 AND PIP2_45. {[9]-p.958}\n<br>*There is and AND relation between PIP2 AND Cdc42 OR PIP2 AND Nck to activate N-WASP. (This is given as actual logic.) {[5]-p.17115}\n\n

*Nck AND PIP2 activate WASP independently of Cdc42 {[14]-p(23388)}\n<br>*Nck forms a complex with WASP {[11]-p(10)}\n<br>*WASP is activate by binding to CDc42 or NCK {[7]-p(578)}\n<br>*Nck and Grb2 activate N-WASP via binding to the proline-rich domain of N-WASP {[2]-p(7)}\n\n

*WASP gets activated by PIP2 and CDC42 {[11]-p(10),[4]-p(97), [19]-p(87)}\n<br>*MLK3 is a downstream effector of Cdc42 {[27]-p.1,[23]-p(768),[12]-p(173)} \n<br>*Cdc42 interacts with WASP {[6]-p.2}\n<br>*WASP is a donwstream of Cdc42. !BUT! WASP is only expressed in hematopoietic cells! {[24]-p.170}\n<br>*WASP is activated by Cdc42 {[21]-p(8),[7]-p(578),[26]-p(175),[25]-p(128), [17]-p(90, 93)}\n<br>*WASP is a target for Rac and Cdc42. {[22]-p(466)}{[18]-p(494)}\n<br>*Cdc42 binds WASP and thereby activates it {[13]-p(5)}\n<br>*WASP has a higher affinity for GTP-bound Cdc42 than GDP-bound. {[8]-p(5685)}. GDP-bound Cdc42 can only partially activate WASP {[8]-p(5690),[14]-p(23387)}\n<br>*N-WASP's self-inhibition is relieved by the cooperative binding of active Cdc42 AND PIP2_45. {[9]-p.958}\n<br>*There is and AND relation between PIP2 AND Cdc42 OR PIP2 AND Nck to activate N-WASP. (This is given as actual logic.) {[5]-p.17115}\n\n

S_135 1 S_19 1 S_118 1 S_85 1 S_153 1 S_132 1 S_75 1 S_244 1 S_19 1 S_118 1 S_85 1 S_153 1 S_132 1 S_75 1 S_132 1 S_244 1 S_135 1 S_19 1 S_118 1 S_85 1 S_75 1 S_153 1 S_75 1

EGFR [4, 7], Src [7], PKC [4, 7, 2], Ca [7, 2] and PA [7] can activate DGK. Because our model also accounts for EGFR dimers, EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4 will be all independent activators. Furthermore, because EGFR signaling continues while EGFR is being internalized [3], the following localizations of EGFR will also be regulators of DGK: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End. However, there are multiple isozymes of DGK that are regulated differently. [4, 7]. Our network will reflect activation pathways by EGFR [4, 7] OR (PKC AND DAG) [6, 4] OR (Ca AND PA AND Src) [7, 2].\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*see PKC.\n\n

*PA is required for DGK-alpha activation {[7]-p(217, 218)} \n<br>*AA can activate DGK {[2]-p(24765)}\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Src activity is nec for the EGFR stimulation of DGK-alpha {[7]-p(217)} (not sure-- inferring from HGF)\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*EGFR may activate DGK {[7]-p(217)}\n<br>*DGK-gamma (or DGK general) could be activated by PKC or CaMK or EGFR {[4]-p(192)}\n\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*PKC activates DGK-theta, but it seems to require the activity of DAG [6]\n<br>*PKC activates DGK-delta {[7]-p(217)}\n<br>*DGK-gamma (or DGK general) could be activated by PKC or CaMK or EGFR {[4]-p(192)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Ca is nec but not suff to activate DGK-alpha. {[7]-p(217)}\n<br>*Ca + RTK (AND) are responsible for activation of DGK-alpha {[7]-p(218)}\n<br>*Ca + PKC are responsible for activation of DGK {[2]-p(24760)} \n \n

*see EGFR_EGFR_EGF_PM above.\n\n

S_194 1 S_16 1 S_174 1 S_139 1 S_30 1 S_99 1 S_157 1 S_214 1 S_227 1 S_195 1 S_240 1 S_18 1 S_66 1 S_29 1 S_244 1 S_56 1 S_229 1 S_52 1

Pix_Cool activation requires PI3P's (the products of PI3K). This is necessary for the localization and/or orientation of Pix_Cool at the membrane [4, 8, 6, 5, 2]. However, PI3P's alone do not fully activate Pix_Cool [4]; B_Parvin binding is necessary as well [9].\nAfter Pix_Cool is at the membrane, the presence of Gbg_i+Pak, Cdc42GTP/GDP, or RacGTP/GDP will cause Pix_Cool to be activated specifically for Rac, nonspecifically for Rac or Cdc42, or inhibited.\nTherefore, the only inputs to Pix_Cool will be PI3P's and B_Parvin. When B_Parvin AND {PIP3_345 OR PIP3_35} are ON, Pix_Cool will be 'ON' and the presence or absence of the elements listed above will be coupled to Pix_Cool in the tables for those elements. \n\n

*beta-parvin interacts/forms a complex with ILK and a-PIX which results in a-PIX activation. b-parvin requires the kinase activity of ILK in order to activate a-PIX {[9]-all}\n

S_74 1 S_186 1 S_54 1 S_186 1

EGFR_Free represents ligand-free, inactive EGFR. The Off state of this node corresponds to non-existing EGFR on cell surface. On the other hand, the On state depicts the presence of ligand-free EGFR, ready to be activated by any of its ligands. To simulate the model under different levels of EGFR expression, this node has an external node - EGFR_Controller - which is responsible for providing the model with inactive EGFR's (hence activates EGFR_Free).<BR>\nUpon binding to their ligand, EGFR dimerizes with other EGFR's or other types of ErbB's. When dimerized, EGFR is removed from the pool of free, inactive EGFR's, therefore the following nodes representing active EGFR dimers act as negative regulators of EGFR_Free (when EGFR_Free was previously ON): [[EGFR_EGFR/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR_EGFR homodimer activated by a ligand-independent process; e.g., GPCR_transactivation), [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR_EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR_EGFR homodimer activated by TGFa), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]], and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]]. ([6, 3, 5, 7, 4, 1])\n\nIn addition, EGFR_Free can be activated by EGFR that are being recycled to the cells surface as inactive EGFR monomers. As mentioned below, this is due the the fact that when activated by TGFa, EGFR_ligand complex is unstable in the endosomal environment and hence the ligand dissociates from the receptor. The receptor is then recycled in an inactive, monomeric form. [2, 6]\n\nAlso, we make EGFR_Free, when active, to remain active (unless any of the negative regulators are on).\n\nWe are making the negative regulators dominant to all positive regulators.\n\n

TGFa-activated EGFR_EGFR dimerization results in removing (i.e., turns off) a EGFR from the EGFR_Free pool.\n\n

EGF_activated EGFR_EGFR dimerization results in removing (i.e., turns off) a EGFR from the EGFR_Free pool.\n\n

EGFR_ErbB2 dimerization results in removing (i.e., turns off) a EGFR from the EGFR_Free pool.\n\n

EGFR_ErbB3 dimerization results in removing (i.e., turns off) a EGFR from the EGFR_Free pool.\n\n

EGFR homodimer activated by ligand-independent processes such GPCR results in removing a EGFR from the EGFR_Free pool.\n\n

EGFR homodimer_ligand complexes activated by TGFalpha are unstable once endocytocised and hence are recycled to the cell surface. EGFRs are recycled as inactive monomers.[]\n\n

S_121 1 S_41 1 S_157 1 S_52 1 S_195 1 S_99 1 S_194 1 S_139 1 S_41 1 S_157 1 S_52 1 S_195 1 S_99 1 S_194 1 S_41 1 S_41 1 S_157 1 S_52 1 S_195 1 S_99 1 S_194 1

MLK2 is activated by Rac OR Cdc42 [6, 4, 2]. \nSAPK phosphorylates MLK2 and appears to be necessary for MLK2-activated apoptosis [3, 5]. However, with no negative regulators of MLK2 activity described, we will not make SAPK sufficient for MLK2 activation. \n\n

*MLK2 and MLK3 interact with Rac-GTP and CDC42-GTP through their CRIB motif {[4]-p(70)}\n\n

*Cdc42 turns on MLK2 {[6]-p(828)}\n<br>*MLK2 and MLK3 interact with Rac-GTP and CDC42-GTP through their CRIB motif {[4]-p(70)}\n\n

S_132 1 S_100 1 S_160 1 S_100 1

Src [7] OR EGFR [7, 10, 2] are negative regulators of PP2A. However, PP2A seems to inactivate Src [1], therefore the effect of Src will fall out of the logic. \ncAMP [10, 8] can activate PP2A. Also, PP2A can reactivate itself [7]; this reactivation is dominant over the negative regulators (if not, PP2A is never ON). \n\nRegarding EGFR: all dimers of EGFR (EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4) will be negaive regulators. Furthermore, because EGFR signaling continues while EGFR is being internalized [4], the following localizations of EGFR will also be regulators of PP2A: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*see EGFR_EGFR_EGF_PM above.\n

*PP2A can be phosphorylated by Src and EGF, resulting in an inactivation {[7]-p(420)}\n<br>*EGF can dephosphorylate PP2A resulting in deactivation {[10]-p(7)}\n<br>*PP2A is negatively regulated by phosphorylation of it Tyr307 by RTKs {[2]-p(80)} \n\n

*PP2A can rapidly re-activate itself in an autodephosphorylation reaction {[7]-p(420)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_195 1 S_43 1 S_66 1 S_43 1 S_139 1 S_43 1 S_52 1 S_43 1 S_194 1 S_43 1 S_227 1 S_43 1 S_30 1 S_43 1 S_43 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_29 1 S_43 1 S_214 1 S_43 1 S_174 1 S_43 1 S_16 1 S_43 1 S_157 1 S_43 1 S_99 1 S_43 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_43 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1

Sos stimulates Ras [17, 54, 53, 8, 11, 39, 49, 24, 51, 6, 40, 20, 15, 50]. RasGRF stimulates Ras [58, 44, 52, 45, 22, 29, 2, 31]. PI3K stimulates Ras [16, 50, 47]. Shp2 stimulates Ras (via p90, which is not in the network) [33, 5, 23]. All of these are OR.\np120Gap is a negative regulator [58, 17, 54, 7, 44, 52, 27, 1, 41] and is not dominant to any of the positive regulators.\n\n\n

*Ras is downstream of RasGRF {[58]-p(3-Fig. 2)}\n<br>*Ras is activated by Ras-GEF (RasGRF) {[44]-p(2-Fig. 1), [52]-p(159), [45]-p(340)}\n<br>*RasGRF is a GEF for Ras family of small GTP-binding proteins {[22]-p(1)}\n<br>*RasGRFs are not specific for Ras. They are GEFs for both Ras and Rac {[29]-p(2), [2]-p(53)}\n<br>*RasGRP1 activates Ras {[31]-p(7961)}\n\n

*SOS and 120Gap as upstreams of Ras {[17]-p(2-Fig. 1), [54]-p(2)}\n<br>*SOS as an upstream of Ras {[56]-p(2-Fig. 1)}\n<br>*Ras is activated by SOS {[8]-p(7), [11]-p(461), [39]-p(2-Fig. 1), [49]-Fig. 3, [24]-p(6-Fig. 3)}\n<br>*SOS activates Ras after it has been moved to the plasma membrane by Grb2 {[51]-p(2)}\n<br>*SOS stimulates the exchange of GTP for GDP on the small G-protein Ras {[6]-p(2, 3), [40]-p(3), [20]-p(322)}\n<br>*SOS enables catalyzation of Ras {[15]-p(1), [50]-p(57)}\n<br>*SOS is able to activate Ras,therefore MAPK pathway {[13]-p(6)}\n<br>*Ras is activated by Ras-GEF (SOS) {[10]-p(2-Fig. 1), [44]-p(2-Fig. 1), [52]-p(159), [36]-p(107), [57]-p(4), [27]-p(41), [14]-p(2-Fig. 1), [55]-p(9)}\n<br>*mSOS can activate Ras {[42]-p(33)}\n<br>*SOS elicits activation of Ras at the plasma membrane {[46]-p(6)}\n<br>*Sos is a GEF of Ras. {[28]-p(2), [2]-p(52), [45]-p(340), [31]-p(7961)} \n<br>*Grb2-Sos complex formation inversely correlates with Ras activation. {[23]-p(8)}\n<br>*Sos is recurited on receptors and activates Ras. {[38]-p(3)}\n<br>*This pathway is RasGRF-independent {[22]-p(3)}\n\n

*SHP2/Gab1 complex is upstream of Ras {[33]-p(4)}\n<br>*SHP2 activates Ras {[5]-p(4)}\n<br>*Shp2 recruits the Grb2-Sos complex to the plasma membrane thereby contributing to the Ras activation. {[23]-p(1)}\n<br>*Shp2 acts upstream of Ras in the induction of Erk activity by EGF. {[23]-p(8)}\n<br>*Shp2 binds Gab1 and dephosphorylates p90, which leads to Ras activation either in a positive stimulatory mechanism or via relief of an inhibitory event. Shp2 subsequently will dephosphorylate its own binding site on Gab1 and dissociate from this complex. {[23]-p(8)}\n

S_161 1 S_69 1 S_198 1

Cortactin is recruited or activated by [[Rac]], [[Src]], [[Fer]], [[Erk]], [[PAK]], [[Dynamin/Epithelial|Dynamin]], [[Actin]] or [[Hip1R/Epithelial|Hip1R]].{[4, 2, 6, 1, 3, 5]}.\n\n

*Cortactin is activated via phosphorylation by Src.{[3]-p(259)}{[2]-p(15)}{[4]-p(2,3)}{[5]-p(648)}\n\n

*Cortactin needs to bind F-actin in order to effectively bind and activate the Arp2/3.{[3]-p(259)} {[2]-p(17)}{[1]-p(4594)} \n\n

*Upon EGF activation, activation of Rac1 leads to cortactin relocalization from internal cytoplasmic regions to the cortical actin network.{[4]-p(3)}\n\n

*Cotractin can be activated by phosphorylation by Erk.{[2]-p(16)}{[5]-p(648)}\n\n

*PAK1 directly phosphorylates cortactin.{[4]-p(3)}\n\n

*Cortactin is activated via phosphorylation by Fer (in PDGF-stimulated fibro-blasts).{[3]-p(259)}{[2]-p(16)}{[4]-p(3)} \n\n

*Dynamin2 binding to cortactin enhances Arp2/3-mediated actin polymerization to a moderate degree.{[4]-p(9)} \n<br>*Dynamin recruits cortactin, which in turn activates the Arp2/3 complex to initiate actin assembly.{[6]-p(1207)} \n\n

*Hip1R binds to cortactin to form a complex, which accelerates the growth of the actin network, hence facilitating the formation of clathrin-coated vesicles.{[6]-p(1208)}\n

S_234 1 S_10 1 S_245 1 S_21 1 S_244 1 S_244 1 S_160 1 S_58 1 S_4 1 S_160 1

AMSH is recruited by STAM (a component of ESCRT_0), ESCRT_III or Alix.{[, 3, 2, 4, 1]} \n\n

*Association with STAM (a component of ESCRT_0) activates AMSH.{[1]-p(365)} \n\n

*Alix mediates the recruitment of the Ub hydrolase degradation of AMSH, UBPY that deubiquitylates MBV cargoes. {[2]-p(645)}\n<br>*AMSH is recruited by Alix.{[4]-p(449)}\n

S_215 1 S_122 1 S_15 1

ErbB3_Y1270 (Tyr_1270 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n\n

ErbB3_Y1270 (Tyr_1270 site of ErbB3) is activated upon receptor dimerization [1].\n\n\n

ErbB3_Y1270 (Tyr_1270 site of ErbB3) is activated upon receptor dimerization [1].\n\n

S_20 1 S_91 1 S_99 1

MLK1 is activated by Rac OR Cdc42 [2]. \n\n

S_160 1 S_132 1

This activation mechanism is only preliminary, thus the following activation mechanism is incomplete.\nalpha_catenin will be defined as ON when beta-catenin is ON and will be able to bind to alpah-catenin as a monomer. The OFF state of alpha_catenin represents the homo-dimeric structure of the protein. alpha_catenin is OFF when beta-catenin is OFF. [1]\n\n

S_235 1

This node represents the homodimer of EGFR activated by EGF on the cell surface. It is activated by both EGF AND EGFR_Free (representation of an inactive EGFR), unless EGFR_T654 is active. [[ErbB2_Free/Epithelial|ErbB2_Free]] is a negative regulator of EGFR_EGFR_EGF_PM (dominant over EGF AND EGFR_Free). EGFR_EGFR_EGF_PM localizes to EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCP will turn EGFR_EGFR_EGF_PM off if it was on in the previous step. \n\n

*EGF activates EGFR {[7]-p(3), [15]-p(1), []-p(4-Fig. 2), [13]-p(1), []-p(1), []-p(2-Fig. 1)}\n<br>*EGFR autophosphorylates at five known tyrosine residues after the addition of EGF {[15]-p(2)}\n<br>*EGF is known to activate EGFR {[11]-p(3)} \n<br>*EGF binds EGFR {[1], <cite>Schoeberl</cite>-p(1)}\n<br>*EGF binds to EGFR which causes dimerization and subsequent cross-phospohrylation of specific residues in the C-terminal tail of teh partnering receptor{[1], <cite>Schoeberl</cite>-p(564)}\n\n

*EGFR_EGFR_EGF_PM is activated by EGFR_Free, which represents a ligand-free EGFR on the cell surface.\n\n

Is ErbB2 is the preferred dimerizing partner for all ErbBs [, 10] -- ErbB2_Free will be a negative regulator of EGFR_EGFR_EGF_PM.\n\n

S_41 1 S_149 1 S_114 1 S_174 1 S_117 1 S_52 1 S_174 1

ErbB2_Y1196 (Tyr_1196 site of ErbB2) is activated when ErbB2 dimerizes with [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] [1].\n\n

ErbB2_Y1196 (Tyr_1196 site of ErbB2) is activated upon receptor dimerization [1].\n

ErbB2_Y1196 (Tyr_1196 site of ErbB2) is activated upon receptor dimerization [1].\n\n

S_91 1 S_220 1 S_195 1

PI3K AND PI4K will turn ON PIP2_34 [10, 13, 25, 9, 2, 20, 7, 21, 23, 22, 24, 3, 12, 18].\nPTEN OR PI5K can turn OFF PIP2_34 by phosphoylation or dephosphorylation conversions [14, 24, 1, 8, 19, 16, 21, 3, 15]. These negative regulators will only turn PIP2_34 OFF if it was ON.\n\n

*PI3K generates PIP2_34 and PIP3_345 {[10]-p(1), [13]-p(2), [25]-p(2905), [9]-p(193), [2]-p(211), [20]-p(968,Fig. 1), [7]-p(1)}\n<br>*PI3K phosphorylates PtdIns-4-P at the position 3 to synthesize PIP2_34. In addition, it can be synthesized by phosphorylation of PIP3 by PI4K {[21]-p(501, 502)}\n<br>*Activation of PI3K leads to generation of PIP2_34 and PIP3_345 {[23]-p(2)}\n<br>*Class II of PI3ks phosphorylate PIP4 to generate PIP2_345 {[22]-p(764), Fig. 1}\n<br>*PI3Ks phosphorylate 3'-OH position of PIP3,PIP2_34,PIP2_35 and PIP3_345 {[24]-p(1)}\n<br>*PI3K phosphorylates PIP4 and PIP2_45 producing PIP2_34 and PIP3_345 {[17]-p(1)}\n\n

*PI4K is able to phosphorylate PI3P to produces PIP2_34 {[3]-p(1), [21]-p(501, 502), [18]-p(78)}\n<br>*PI4K employs PIP3 as a substrate to synthesize PIP2_34 {[6]-p(235)}\n<br>*PI4Ks convert PtdIns to PIP4 thus generated can be further phosphorylated by both PI3K and PI5Ks to yield PIP2_34 or PIP2_45,respectively.{[21]-p(492)}\n<br>*PI3K phosphorylates PtdIns-4-P at the position 3 to synthesize PIP2_34. In addition, it can be synthesized by phosphorylation of PIP3 by PI4K {[21]-p(501, 502)}\n<br>*PIP2_34 is a product of PI3K from PIP_4 {[20]-p(968), Fig. 1}\n\n

*PTEN (3'-phosphatase) converts PIP2_34 to PIP_4 and PIP3_345 to PIP2_45 {[24]-p(1), [1]-p(2), [14]-p(3)}\n<br>*PTEN dephosphorylates PIP2_34 and PIP3_345 at position 3 {[8]-p(1), [19]-p(4)}\n<br>*PTEN catalyzes dephosphorylation of PIP3_345 and PIP2_34 at the D position {[16]-p(1)}\n\n

*PI5K converts PIP2_34 to PIP3_345 in vitro {[21]-p(498), [3]-p(1), [15]-p(88)}\n<br>*PI5K also produces PIP2_34 nad PIP2_35 from PI3P {[3]-p(1), [15]-p(88)}\n<br>*PI5K can also phosphorylate PIP2_34 at 5-position and is likely responsible for PIP3 synthesis during oxidative stress in intact cells. {[15]-p(91)}\n\n

S_208 1 S_219 1 S_54 1 S_54 1 S_196 1 S_106 1

alpha-s_R is stimulated by its ligand alpha-s_lig. GRK phosphorylates alpha-s_R, but this has no effect on its own [13, 4, 2, 6, 12]. When GRK does phosphorylate alpha-s_R, B_Arrestin has to be ON in order to turn alpha-s_R OFF [10, 1]. GRK only phosphorylates alpha-s_R when alpha-s_R is ON [4], so alpha-s_R will be an input to itself.\nThe external inputs will not be dominant to the negative regulators (otherwise the negative regulators really have no effect). \nNote, our GPCRs are separated into two nodes so that more realistic and precise simulation can be conducted. Since the phosphorylation of GPCRs and the sequestering by B_Arrestin are two seperate events, we have a phosphorylated version of each GPCR. This phosphorylated GPCR (Palpha-q_R,Palpha-12_13_R, etc.) has its own logic table and acts as a node on its own during the simulations.\n\n

*B-arrestin down-regulates GPCR by interrupting the interaction between the receptor and the G-prot. {[10]-p(1534), [5]-all}\n<br>*Membrane recycling can turn off GPRC {[10]-p(1534)}\n<br>*b-arresins desensitizes 7MSRs by structurally blocking their interaction with G-prot. {[1]-p(1), [5]-all}\n<br>*b-arrestins uncouple the receptor from the G prot. and may target many GPCRs for internalization in specialized membrane areas {[9]-p(1940)}\n\n

S_55 1 S_95 1 S_141 1 S_141 1 S_187 1 S_55 1 S_187 1 S_95 1 S_141 1 S_141 1 S_187 1 S_55 1 S_141 1 S_95 1 S_95 1 S_141 1 S_141 1 S_187 1 S_55 1

PLD creates/activates PA [19, 7, 5, 4, 8, 13, 14, 12, 15, 1, 9, 17, 2, 22, 16, 18, 20] when PA is OFF.\nAlternatively, PA can be produced from DAG with the help of DGK [19, 7, 3, 17, 6], however the PA produced frrom DAG is polyPA, which is not the same as monoPA produced by PLD. MonoPA seems to be the one regulating the Rho pathway [7, 11, 10] \n\n

*PA is produced by PLD {[19]-p(1), [7]-p(2), [5]-p(1), [4]-p(35), [8]-p(1), [13]-p(251), [14]-p(2), [12]-p(140), [15]-p(33818), [1]-p(1234), [9]-p(140), [17]-p(28252), [2]-p(7848), [22]-p(26209), []-p(226)}\n<br>*PLD catalyses the hydrolysis of phosphatidylcholine to generate PA {[16]-p(1), [18]-p(1), [1]-p(1234), [20]-p(6), []}\n<br>*PLD stimulates further synthesis of PIP2_45 via PA stimulation of PI5K {[13]-p(245), []}\n

S_138 1

ErbB2_Y1023 (Tyr_1023 site of ErbB2) is activated when ErbB2 dimerizes with [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] [1].\n\n

ErbB2_Y1023 (Tyr_1023 site of ErbB2) is activated upon receptor dimerization [1].\n

ErbB2_Y1023 (Tyr_1023 site of ErbB2) is activated upon receptor dimerization [1].\n\n

S_91 1 S_220 1 S_195 1

tion Mechanism==\n[[E-cadherin]] AND [[p120_catenin]] are activators of Fer [1].\n\n

*Phosphorylated p120_catenin increases the binding of Fer/Fyn-p120ctn-E-cadherin complex [1].\n<br>*p120_catenin brings Fer to N-cadherin [1].\n\n

S_126 1 S_90 1

MEKK1 [3, 9, 4, 7, 2] OR MEKK2 [10] OR MEKK3 [7, 9, 10] OR MEKK4 [7, 9, 2] MLK1 [7] OR MLK2 [7] OR MLK3 [7] can activate MKK7. ASK1 can also activate MKK7 [8, 1, 7, 6, 9], and since ASK1 is required for p38/SAPK activation, ASK1 will be in an AND with the other activators. \n\n

*Mekk2 activates MKK7. {[10]-p(661)}\n\n

*ASK1 phosphorylates and activateds MKK4 or MKK7 and MKK3 or MKK6 {[8]-p(893, 897), [1]-p(1059), [7]-p(822), [6]-p(1), [9]-p(187), Fig. 1} \n<br>*ASK1 is necessary for the sustained activation of p38/SAPK, so it is likely necessary for Sek1 activation. {[5]-p(263)}\n\n\n

*MEKK4 can activate MKK7 {[7]-p(822), [9]-p(187), Fig. 1}\n<br>*MEKK5 is involved in activation of MKK7 {[2]-p(7)}\n\n

*MKK4/7 is activated by MEKK1 {[3]-p(3), Fig. 1, [9]-p(187), Fig. 1}\n<br>*Sek1 is phosphorylated and activated by Mekk1 and MKK7 {[4]-p(3), [7]-p(822)}\n<br>*MKK7 is suggested downstream of MEKK1, because when dominant negative expression, MEKK-stimulated JNK activity is inhibited {[2]-p(7)} \n\n

*MEKK3 can activate MKK7 {[7]-p(822), [9]-p(187), Fig. 1, [10]-p(662)}\n\n

S_216 1 S_236 1 S_204 1 S_236 1 S_6 1 S_236 1 S_150 1 S_236 1 S_42 1 S_236 1 S_120 1 S_236 1 S_49 1 S_236 1

Cbp is a required positive regulator of Csk[14, 8, 16], thus the following activators are in an AND with Cbp. Fak AND Src also activate Csk by Paxillin phosphorylation [2, 5, 10]. PKA [1, 9, 6] OR Gbg_i OR Gbg_12_13 OR Gbg_q [13, 6, 12] are also positive regulators of Csk. \nSHP2 is a negative regulator, dominant to Fak AND Src activators [7].\n\n

*Fak and Src phosphorylate Pax on Y31 nad Y118 that then provide a binding site for Csk. {[2]-p(1322)}\n\n

*Cbp recruits/activates Csk {[16], [8], <cite>Roskoski</cite>-p(9)} \n<br>*Dephosphorylation (activation) of PAG (Cbp) by SHP2 is required for normal gorwth factor evoked SFK activation. {[8]-p.346}. This is also true for integrin stimulation {[8]-p.349}\n\n

* \n<br>*PKA can phosphorylate and activate the Csk {[1]-p(165),[6]} \n<br>*PKA induces a 2-4 fold incrase in phosphotransferase activity of Csk in lipid rafts of T-cells through phosphroylation of Ser_364 in Csk {[9]-p(19)}\n\n

*Shp2 dephosphorylates Pax and displaces it from Csk [7]\n\n

S_63 1 S_222 1 S_89 1 S_148 1 S_133 1 S_198 1 S_222 1 S_89 1 S_148 1 S_133 1 S_135 1 S_244 1 S_63 1 S_198 1

IL-1_TNFR is stimulated by IL1_TNF. \n\n

S_181 1

For Cbl_RTK, {EGFR_Y1045 OR Grb2} AND Src are activating, (Spry2 AND CIN85) OR EGFR_T654 are negative regulators of Cbl_RTK, (Pix/Cool AND Cdc42 AND Src) are negative to Cbl_RTK and positive to Cbl_FA because it sequesters Cbl away from RTK and to focal adhesions (FA). Cbl_FA is also a negative regulator. All of these negative regulators are dominant to the positive regulators [6, 5].\n\n

*Src can phosphorylate Cbl_FA, which activates it {[6], p. 911}.\n<br>*When Src phosphorylates Cbl, Cbl becomes sequestered from EGFR and EGFR becomes very stable (which can even cause transformation) {[5], p. 33}.\n<br>*Src is constitutively associated with Cbl {[6], p. 915}.\n<br>*Cbl is localized to FA's, probably due to Src {[6], p. 915}.\n<br>*When Src phosphorylates Cbl, it allows PI3K, Fak, CrkL to associate with Cbl {[6], p. 915}.\n<br>*Src+Cbl is essential for FA creation {[6], p. 915}.\n\n

S_244 1 S_132 1 S_40 1 S_81 1

SHP2 is a dominant negative regulator of Cbp [3, 2].\nSrc activates Cbp [4].\n\n

*Src phosphorylates and activates Cbp [4]\n\n

*Shp2 negatively regulates PAG (recruiter of Csk) and is a dominant negative regulator. {[2]-all} \n<br>*Shp2 reverses or prevents Tyr527 phosphorylation of Src. This is done indirectly through inhibiting the recruiter of Csk. {[3]-p(8), [2]-all} \n<br>*SHP2 dephosphoprylates and inactivates Cbp {[1]-p(5351)}\n\n

S_244 1 S_198 1

This node represents an ubiquitinated activated homodimer of EGFR. Upon activation of EGFR by ligand binding, Cbl is activated and ubiquitinates EGFR. Therefore, EGFR_Ub is activated by (EGFR_EGFR_EGF_PM AND Cbl) OR (EGFR_EGFR_TGFa_PM AND Cbl).\nWhen EGFR is recruited into CCPs, EGFR_EGFR_EGF_CCP or EGFR_EGFR_TGFa_CCP will replace EGFR_Ub. Therefore, EGFR_EGFR_EGF_CCP OR EGFR_EGFR_TGFa_CCP acts as a negative regulator of EGFR_Ub.\n\n

*EGFR_Ub is activated by EGFR_EGFR_TGFa_PM, which represents EGFR activated by TGFa on the plasma membrane. \n\n

*EGFR_Ub is activated by EGFR_EGFR_EGF_PM, which represents EGFR activated by EGF on the plasma membrane. \n\n

*Activaton of EGFR_EGFR_EGF_CCP results in removing (i.e., turns off) EGFR_Ub.\n

*Activaton of EGFR_EGFR_TGFa_CCP results in removing (i.e., turns off) EGFR_Ub.\n\n

S_52 1 S_81 1 S_174 1 S_30 1 S_157 1 S_81 1 S_174 1 S_30 1

This node represents TGFa-activated homodimer of EGFR localized in clathrin-coated vesicles. CCPs are pinched off from the plasma membrane by a [[Dynamin/Epithelial|Dynamin]] and [[Actin]]-dependent mechanism {[3, 2]}. Since EGFR_EGFR_TGFa_CCV inherits [[PIP2_45]], [[AP2/Epithelial|AP2]] and [[Clathrin]] from [[EGFR_EGFR_TGFa_CCP/Epithelial|EGFR_EGFR_TGFa_CCP]], EGFR_EGFR_TGFa_CCV will be activated by (EGFR_EGFR_TGFa_CCP AND Dynamin AND Actin AND PIP2_45 AND AP2 AND (Clathrin OR GAK)). Furthermore, once CCVs fuse with early endosomes, EGFR_EGFR_TGFa_CCV will be replaced by [[EGFR_EGFR_TGFa_End/Epithelial|EGFR_EGFR_TGFa_End]], EGFR_EGFR_TGFa_End acts as a negative regulator of EGFR_EGFR_TGFa_CCV when it was previously active.\n\n

*Activated EGFR is entrapped in clathrin-coated vesicles by a dynamin and actin-dependnet pinching off mechanism. {[3]-p(610)}{[2]-p(1531)}\n\n

*PIP2_45 is considered as an upstream node since EGFR_EGFR_TGFa_CCV inherits it from EGFR_EGFR_TGFa_CCP, and PIP2_45 will bind to GAK, the downstream node of EGFR_EGFR_TGFa_CCV.\n\n

*Activated EGFR is entrapped in clathrin-coated vesicles by a dynamin and actin-dependnet pinching off mechanism. {[3]-p(610)}{[2]-p(1531)}\n\n

*Auxilin (GAK) promotes the assembly of clathrin into CCVs.{[1]-p(641)} \n\n

*Clathrin is considered as an upstream node since EGFR_EGFR_TGFa_CCV inherits it from EGFR_EGFR_TGFa_CCP, and Clathrin will bind to GAK, the downstream node of EGFR_EGFR_TGFa_CCV.\n\n\n

*AP2 is considered as an upstream node since EGFR_EGFR_TGFa_CCV inherits it from EGFR_EGFR_TGFa_CCP, and AP2 will bind to GAK, the downstream node of EGFR_EGFR_TGFa_CCV.\n\n

*EGFR_EGFR_TGFa_CCV is activated by EGFR_EGFR_TGFa_CCP, which represents dymerized and activated EGFR in a clathrin-coated pit.\n\n

Activaton of EGFR_EGFR_TGFa_End results in removing (i.e., turns off) EGFR_EGFR_TGFa_CCV. \n\n

S_66 1 S_139 1 S_30 1 S_118 1 S_159 1 S_4 1 S_10 1 S_11 1 S_183 1

alpha-i_R is stimulated by its ligand alpha-i_lig. GRK phosphorylates alpha-i_R, but this has no effect on its own [10, 6, 4, 9, 8]. When GRK does phosphorylate alpha-i_R, B_Arrestin has to be ON to turn alpha-i_R OFF [5, 1]. GRK only phosphorylates alpha-i_R when alpha-i_R is ON [6], so alpha-i_R will be an input to itself.\nThe external inputs will not be dominant to the negative regulators (otherwise the negative regulators really have no effect). \nNote, our GPCRs are separated into two nodes so that more realistic and precise simulation can be conducted. Since the phosphorylation of GPCRs and the sequestering by B_Arrestin are two separate events, we have a phosphorylated version of each GPCR. This phosphorylated GPCR (Palpha-q_R,Palpha-12_13_R, etc.) has its own logic table and acts as a node on its own during the simulations.\n\n

*B-arrestin down-regulates GPCR by interrupting the interaction between the receptor and the G-prot. {[5]-p(1534), [7]-all}\n<br>*Membrane recycling can turn off GPRC {[5]-p(1534)}\n<br>*b-arresins desensitizes 7MSRs by structurally blocking their interaction with G-prot. {[1]-p(1), [7]-all}\n<br>*b-arrestins uncouple the receptor from the G prot. and may target many GPCRs for internalization in specialized membrane areas {[2]-p(1940)}\n\n

S_80 1 S_95 1 S_231 1 S_231 1 S_80 1 S_67 1 S_67 1 S_95 1 S_231 1 S_231 1 S_80 1 S_67 1 S_231 1 S_95 1 S_95 1 S_231 1 S_231 1 S_80 1 S_67 1

CamKK and CaM are activatiors of CaMK [2, 5, 4, 8], in an AND relationship [5]. PP2A is a negative regulator [7, 1, 6, 3, 4], but is not dominant to the stimulators above [5].\n\n

*CaM kinase is regulated by Ca/CaM complex. After the binding, the intrinsic autoinhibition is releived and CaM-bound subunit becomes fully active {[8]-p(2)}\n<br>*CaM binds CaMK {[5]-p(1)}\n

*PP2A can dephosphorylate activated preperations of CaM kinase I, II and IV. {[7]-p(3)}\n<br>*CaMK IV binds to PP2A {[7]-p(2, tab.2)}\n<br>*CaMK IV can form a complex with PP2A {[1]-p(5)}\n<br>*PP2A can modulate the activities of CAMK {[6]-p(428)}\n<br>*PP2A activity inhibited the activation of CamKIV, and inhibition of PP2A lead to increased Ca-stimulated activity of a CamIV-dependent promoter. {[3]-p(4)}\n<br>*PP2a negatively regulates CaMKIV.\n<br>*Activated CaMKIV is dephosphorylated and deactivated by PP1,PP2A,PP2B and PP2C {[4]-all}\n\n

S_223 1 S_3 1

PIP2_45 is a negative regulator of Sos, because when it binds Sos's PH domain, it keeps it closed and OFF [27] but has no effect in the activation process. When PI3K is active, it makes PIP3_345 which is necessary for Sos activity [3, 9, 27, 14].\nHowever, activation of Sos is not sufficient for biological activity since is is also necessary that Sos be localized to the membrane. Thus, in this model Sos is defined as ON when it is active AND localized.\nGrb2 can localize Sos [8, 1, 22, 4, 6, 24, 2, 20, 11], as can Nck AND Crk [10]. Therefore, Grb2 OR {Nck AND Crk} are necessary for activation of Sos [10].\nErk breaks up the Grb2-Sos complex, so it will be a dominant negative to that pathway, but not the Nck/Crk pathway [12, 28]. Cbl is also negative regulator to the Grb2/Sos pathway [27].\nRas itself is necessary for maximal activation of Sos, but since Sos can become active without it, it will fall out of the logic [29]. \n\n

*SOS creates a complex witg Grb2 {[8]-p(7), [1]-p(5-Fig. 1), [22]-p(2), [4]-p(1)}\n<br>*Grb2 recruits SOS from the cytosol to the plasma membrane without affecting its GAP activity,but it's not certain whether Grb2 also activates SOS or only recruits it {[25]-p(159)}\n<br>*Grb2 SH3 domains constitutively bind polyproline SH3 motifs on mSos {[16]-p(33)}\n<br>*Sos binds predominantly to Grb2 {[6]-p(4)}\n<br>*Grb2 binds and recruits SOS to the plasma membrane {[24]-p(2)}\n<br>*There seems to be competition between Gab1 and Sos for Grb2 binding upon EGF stimulation. {[2]-p(7)}\n<br>*Binding of Grb2 to phosphorylated EGFR results in the recruitment of Sos. {[20]-p(3)}\n<br>*SOS creates a complex with Grb2 {[8]-p(7), [11]-p(2-Fig. 1)}\n\n

*Erk as an upstream of SOS {[15]-p(2-Fig. 1), [7]-p(2-Fig. 1)}\n<br>*SOS can by phosphorylated by activated Erk to maintain a feedback inhibition loop {[18]-p(3), [21]-p(89)}\n<br>*Erk is responsible for the phosphorylation of SOS and disassociation of Grb2-Sos complex. {[28]-p(1), [12]-p(6357)}\n<br>*Erk overexpression results in hyperphosphorylation of SOS in vivo. {[26]-p(4)}\n<br>*Erk 1, 2 inhibits SOS {[19]-Fig. 3}\n\n

*SOS can be bound by Nck and Crk adaptor proteins {[10]-p(12)}\n\n

S_85 1 S_153 1 S_74 1 S_19 1 S_74 1 S_81 1 S_153 1 S_234 1 S_118 1 S_85 1 S_19 1 S_74 1

Rab5 recruits Rabaptin_5 to early endosomes.{[4]-p(3747)}\n\n

*Rabaptin_5 is a Rab5 effector and can be recruited from cytosol onto both CCV and early endosome membranes.{[4]-p(3747)}{[5]-p(1941)}{[1]-p(109)} \n<br>*Rabaptin_5 down-regulates Rab5 GTPase activity. This is achieved both by direct inhibition and by Rabaptin_5 associating with Rabex_5.{[3]-p(698)} \n<br>*Rabaptin_5 stabilizes Rab5 in GTP-bound active form by down-regulating GTP hydrolysis.{[5]-p(1941)} \n

S_192 1

Graf is activated by Fak {[6, 4, 3, 8, 7]}. Fak must be phosphorylated by Src for Graf to be activated so Fak is AND with Src. \n\n

*FAK provides binding sites for CAS and Graf {[6]-p(2)}\n<br>*Graf is bound by Fak to inhibit Rho {[6]-p(14), Fig.7}\n<br>*Cas binds to FAK through its SH3 domain {[4]-p(1), [7]-p(1411)} \n<br>*Graf binds to FAK {[8]-p(442), Fig.3, [1]-p(9576)}\n<br>*Graf associates with FAK {[3]p(12)}\n<br>*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[5]-p(3584)}\n<br>*Fak contains a binding site for p130Cas, Graf, and Arf-GAP. {[9]-p(2), [2]-p(2689-Fig.8)}\n \n\n

S_135 1 S_244 1

This node represents the homodimer of EGFR activated by EGF in the intralumenal vesicles of MVB, which is destined to lysosomal degradation. Rab7 is involved in this process of early-to-late endosome maturation.{[3, 5]}\nUbiquitinated EGFR is recognized and sorted into the intralumenal vesicles of MBV by sequential activities of ESCRT complexes, [[Alix/Epithelial|Alix]] and [[VPS4/Epithelial|VPS4]].{[, 7, 6, 2]} Furthermore, Eps15 associating with Hrs (a component of ESCRT_0) provides additional means to recruit ubiquitinated EGFR.{[2]} Therefore, EGFR_EGFR_EGF_Lysosome is activated by ([[EGFR_EGFR_EGF_MVB/Epithelial|EGFR_EGFR_EGF_MVB]] OR [[ESCRT_III/Epithelial|ESCRT_III]]) AND [[Rab7/Epithelial|Rab7]] AND Alix AND(VPS4 OR [[Eps15/Epithelial|Eps15]]). In addition, [[AMSH/Epithelial|AMSH]] acts as a negative regulator of EGFR_EGFR_EGF_Lysosome since AMSH promotes recycling from endosomes{[]}. Because with AMSH, in this model, EGFR never goes to lysosome (which, in literature, is thought of as a canoNIKal pathway, the model has AMSH as a regulator with no effect on EGFR_EGFR_EGF_Lysosome).\n\n

*EGFR_EGFR_EGF_LE is activated by EGFR_EGFR_EGF_MVB, which represents dymerized, activated and ubiquitinated EGFR in a sorting endosome.\n\n\n

*Concerted action by ESCRTIII and VPS4 leads to membrane constriction and fission necessary for the creation of ILV, which is to be targeted for lysosomal destruction.{[]-p(158)}\n<br>*Vps4 function is required for the formation of ILVs.{[]-p(364)}\n\n

*ILVs bud off from MVBs by recruiting Alix, ESCRTI-III and TSG101 (ESCRT_0). Eventually, MVBs fuse with lysosomes and intravesicular proteins are degraded.{[6]-p(911)}\n\n

*Rab7 is essential for transport from early to late endosomes.{[3]-p(184)} \n<br>*Early-to-late endosome maturation involves the acquisition of Rab7.{[5]-p(610)}\n\n

*The ESCRT_III complex might function downstream of internalization to ILVs.{[]-p(568)}{[]-p(1530)} \n<br>*ESCRTs 0, I, II and III catalyse receptor sorting at endosomal membranes into vesicles that bud off from the limiting membrane into the lumen of the endosome giving rise to MVBs. MVB cargo is then directed to late endosomes where it is routed into lysosomes for degradation.{[]-p(156)}\n\n

*Eps15 associating with Hrs provides additional means to recruit ubiquitinated EGFR.{[2]-p(687,689)}\n\n

S_102 1 S_144 1 S_225 1 S_122 1 S_124 1 S_16 1 S_122 1 S_124 1 S_144 1 S_225 1

Shc is defined ON, when it can bind downstream signaling components. Because this ability to bind downstream effector largely depends on the phosphorylation state of Shc's Tyr_317 site, Shc will be ON when it is phosphorylated at the site (and hence can transduce the signal downstream). Because Src [29, 14, 5, 17, 19, 13, 28, 6], FAK [14, 11, 24, 13, 15, 25], as well as EGFR [26, 18, 1, 24, 20] phosphorylate Shc on Tyr317, they will activate Shc. However, in the case of EGFR, because the phosphorylation process of Shc by the receptor is dependent on its ability to bind to one of 1) three sites on EGFR (Y1173, Y1148, Y992), 2) three sites on ErbB2 (Y1196, Y1221/22, Y1248), 3) Y1309 on ErbB3, 4) two sites on ErbB4 (Y1188, Y1242), these sites will be in an AND relation with EGFR. In addition, in our model, to capture a higher level of dynamics of the EGFR dimerization and signaling pathways, we represent the receptor as multiple nodes, depending on the dimerization partner, as well as the localization of the receptor [10]. Therefore, the above EGFR sites will be in an AND relation with the following EGFR nodes (which are mutually in an OR relationship): EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End, EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4. Finally, PTEN dephosphorylates and hence inhibits Shc [23, 16, 9, 2, 3, 30]. \n\n\n

*see EGFR_Y1173 above.\n\n

*Shc binds to ErbB3 [26].\n\n

*see EGFR_Y1173 above.\n\n

*Shc binds to ErbB4 [26].\n\n

*see EGFR_Y1173 above.\n\n

*Shc is affected by activity of Src {[29]-p(2)}\n<br>*Activated Src can phosphorylate Shc on Y239,240 and 317 which provide binding sites for downstream effectors such as Grb2 {[14]-p(6)}.\n<br>*Shc may be activated by Src {[5]-p.17(137)}\n<br>*Src links Gbg to activation of the Ras-MAPK pathway through phosphorylation of Shc and the recruitment of Grb2 and SOS {[17]-p(2)}\n<br>*Shc is phosphorylated by Lyn(Src) {[19]-p(1172), Fig. 2}\n<br>*c-shr can phosphorylate shc {[13]-p(458), Fig. 6}\n<br>*Src regulates Shc phosplorylation {[13]-p(468), Fig. 9}\n<br>*Shc is a substrate of Src {[28]-p(123)}\n<br>*The dual FAK-Src PTK complex promotes the tyrosine phosphorylation of SHC, Pax, and p130Cas {[6]-p(2)}\n<br>*The phosphorylation of Shc by Src appears to be dependent on active EGFR which brings Shc to the plasma membrane [7]\n\n

*see EGFR_Y1173 above.\n\n

*Shc binds to ErbB2 [26].\n\n

*see EGFR_Y1173 above.\n\n

*see EGFR_Y1173 above.\n<br>*EGFR_Y992, when phosphorylated, is a (minor; Y1173 was found to be the major one) binding site to Shc []\n\n

*see EGFR_Y1173 above.\n\n

*Shc binds to ErbB4 [26].\n\n

*see EGFR_Y1173 above.\n\n

*The regulatory information of Shc by EGFR in this section applies to all EGFR_related subsections below. Because Shc binds to specific phosphorylation sites on EGFR (and other ErbBs), these sites are upstream regulators of Shc. In addition, as described below, Shc's activity is also regulated by its phosphorylation mediated by EGFR kinase, as well as all other receptors [12]. Therefore, all localizations of EGFR, as well as dimerization combinations of all ErbBs will be (mutually independent) inputs to Shc.\n<br>*Shc binds to EGFR_pY1173 and pY1148 and is subsequently phosphorylated by the EGFR kinase {[26]-p(2)}\n<br>*Shc an EGFR bind to each other when phosphorylated {[18]-p(1), [1]-p(5-Fig. 1)}\n<br>*Shc increases its mitogeNIK signalling after EGF stimulation {[1]-p(4)}\n<br>*Shc is tyrosine phosphorylated by receptor activation and it subsequently interacts with Grb2 {[24]-p(4)}\n<br>*Shc binds to activated EGFR. {[20]-p(1)}\n\n

*Shc binds to ErbB2 [26].\n\n

*Fak can phosphorylate Shc on Y317 which provides a binding site for Grb2 {[14]-p(6)}\n<br>*Shc is phosphorylated by activated FAK {[11]-p(12), [25]-p(2689)}\n<br>*Shc is a substrate of FAK {[24]-p(5)}\n<br>*Shc is directly binded to and phosphosphoralted by FAK {[13]-p(442, 444, 457), Fig. 3, Fig. 6}\n<br>*Shc associates with FAK {[15]-p(1)}\n\n

*see EGFR_Y1173 above.\n\n

*PTEN dephosphorylates FAK and Shc {[23]-p(2), [16]-p(3), [9]-p(5), [2]-p(6)} which leads to inhibition of cell migration {[2]}\n<br>*PTEN dephosphorylates SHC {[3]-p(1), [19]-p(1174)}\n<br>*The dephosphorylation of Shc by PTEN inhibited the recruitment of Grb2, which leads to downregulation of MAP kinases. {[30]-p(36)}\n\n

*see EGFR_Y1173 above.\n\n

[12] mentions only EGFR and ErbB2 as RTKs that phosphorylate Shc, but we will assume that ErbB4 has the same capability (we'll need a ref. for ErbB4 though) due to the fact that ErbB4 also has binding sites for Shc [26]\n\n

S_163 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_170 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_53 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_167 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_113 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_77 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_135 1 S_196 1 S_13 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_190 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_76 1 S_16 1 S_157 1 S_220 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_20 1 S_196 1 S_244 1 S_196 1

PI3K AND PIP2_45 can activate PIP3_345 [20, 36, 43, 37, 54, 17, 35, 11, 52, 59, 1, 24, 49, 41, 40, 58, 14, 18, 21, 13, 45, 29, 57, 2, 56, 34, 26, 30, 25, 10, 33, 7, 44, 12, 27, 15, 8, 47, 3, 55].\nPI5K AND PIP2_34 can also activate [25, 4, 33].\nPTEN is a negative regulator, but only if PIP3_345 was ON [6, 57, 50, 48, 32, 31, 26, 58, 29, 56, 16, 28, 54, 55, 38, 4, 12, 1, 33, 42, 53, 19, 5, 51]. PIP3_345 turns OFF if no stimuli is present [54].\n\n

*PIP3_345 is produced by PI3K {[20]-p(2),fig1, [36]-p(39, 46), [43]-p(4), [37]-p(41), fig.6, [54]-p(1170), Fig. 1, Fig. 2}\n<br>*PIP3_345 is produced by PI3K {[17]-p.2(828), [35]-p(534), [36]-p(5), [11]-p(4), [52]-p(1), [59]-p(2905, 2909), [1]-p(215), Fig. 2, [24]-p(968), Fig. 1, [49]-p(8), [41]-p(1), [40]-p(64-Fig. 5), [58]-p(1), Fig. 1}\n<br>*PI3K synthesises PI3_345 {[14]-p(1), [18]-p(1), [21]-p(357)}\n<br>*PI3K generates PIP2_34 and PIP3_345 {[13]-p(1), [45]-p(2)}\n<br>*Activation of PI3K leads to generation of PIP2_34 and PIP3_345 {[29]-p(2), [57]-p(2)}\n<br>*After activation of PI3K, the PH domain binds PIP3_345 {[2]-p(1)}\n<br>*PI3Ks phosphorylate 3'-OH position of PIP3,PIP2_34,PIP2_35 and PIP3_345 {[56]-p(1)}\n<br>*PI3K can stimulate Rac activity through its product PIP3_345, which binds to Tiam, which is a GEF for Rac. {[34]-p(3)}\n<br>*PI3K activation by growth factors results in an increase in PIP3_345, whichs leads to the translocation of Akt to the membrane. \n<br>*Activation of PI3K leads to production of PIP3_345, which promotes further membrane recruitment of Gab1, and additional enhancement of PI3K signaling. {[26]-p(1455)}\n<br>*PIP2_45 is a precursor for PIP3_345 {[17]-p.2(282), [25]-p(502), [10]-p(1), [33]-p(2)}\n<br>*PIP2_45 is converted to PIP3_345 by PI3K {[7]-p(1), [54]-p(1170), Fig. 1, Fig. 2, [44]-p(1), [12]-p(193, 195)}\n<br>*PIP3_345 is downstream of PIP2_45 {[27]-p(2), Fig. 2}\n<br>*PI3K phosphorylates PIP2_45 to produce PIP3_345 {[15]-p(3), Fig. 1, [8]-p(2), [47]-p(2), [25]-p(502), [2]-p(6), [3]-p(2), [24]-p(968), Fig. 1, [58]-p(1), Fig. 1}\n<br>*PIP3_345 is generated via phosphorylating PIP2_45 by class I of PI3k {[55]-p(764, 765), Fig. 1}\n<br>*Activated PI3K catalyzes the phosphorylation of PIP2_45 at the 3' position of the inositol ring to produce PIP3_345 {[30]-p(3473), Fig. 2}\n<br>*PI3K phosphorylates PIP4 and PIP2_45 producing PIP2_34 and PIP3_345 {[23]-p(1)}\n\n

*PI5K converts PIP2_34 to PIP3_345 in vitro {[25]-p(498), [4]-p(1)}\n<br>*PIP3_345 can also be generated from PIP2_34 by PI5K {[33]-p(2)}\n<br>*PIP3_345 is produced when PI5K and PIP3 are mixed together. The amount of PIP3_345 is significant {[25]-p(498)}\n<br>*PIP3_34 is a poor substrate for PI5K, but PI5K can doublephosphorylate PIP3 to synthesize PIP3_345 {[22]-p(78)}\n\n

*PIP3_345 is a substrate of PTEN: PTEN can remove a specific phosphate group from PIP3, thereby inhibiting Akt {[6]-p(2, 3)}\n<br>*PIP3_345 is a substrate of PTEN {[57]-p(2)}\n<br>*PTEN can dephosphorylate PIP3_345 to stop PI3K activity {[50]-p(2), [48]-p(5), [32]-p(29), [31]-p(1), [26]-p(1448), [58]-p(1), Fig. 1, [5]-p(278)}\n<br>*PTEN decreases the level of PIP3 and prevents Akt activation {[48]-p(4), [32]-p(29), []-p(1)}\n<br>*PTEN limits PIP3_345 which is necessary for Act activity {[29]-p(5)}\n<br>*PTEN (3'-phosphatase) converts PIP2_34 to PIP_4 and PIP3_345 to PIP2_45 {[56]-p(1), [16]-p(3)}\n<br>*PTEN catalyzes dephosphorylation of PIP3_345 and PIP2_34 at the D position {[28]-p(1)}\n<br>*PTEN breaks PIP3_345 down to PIP2_45 {[54]-p(1170), Fig. 1, [55]-p(763, 765), Fig. 1}\n<br>*PTEN can dephosphorylate PIP3_345 {[4]-p(4), [12]-p(197)}\n<br>*PIP3_345 is converted to PIP2_45 by PTEN {[1]-p(215), Fig. 2, [33]-p(2), [54]-p(1)}\n<br>*PTEN decreases PIP3_345 in response to growth factors. {[]-p(1)}\n<br>*PTEN dephosphorylates PIP3_345 and is able ot inhibit EGFR signaling and translocation of Gab1. {[26]-p(1449)}\n<br>*PTEN catalyzes dephosphorylation of PIP3_345 at position 3 on the inositol ring; This produces a substrate that can be recycled by PI3K {[42]-p(3), [53]-p(3), [51]-p(88)}\n<br>*PTEN decreases the level of PIP3 {[33]-p(2)}\n<br>*Cells that lack PTEN have elevated levels of PIP3_345. {[19]-p(1)}\n\n

S_106 1 S_54 1 S_196 1 S_74 1 S_219 1 S_118 1 S_196 1 S_74 1

Integrins AND ECM activate PTPPEST [2]. \nPKC OR PKA are negative regulators of PTPPEST [1, 2].\nWe make them dominant because the phosphorylation state of PTPPEST is not known when regulated by integrins [2].\n\n

*Integrins activate PTP-PEST when bound to ECM {[2]}\n\n

*PKC phosphorylates and inhibits PTPPEST {[2]-p(7312)} \n\n

*PTPPEST is phosphorylated and inhibited by PKA {[1]-p(166), [2]-p(4312)}\n\n

S_200 1 S_23 1 S_133 1 S_240 1

ErbB4_Y1242 (Tyr_1242 site of ErbB4) is activated when ErbB4 dimerizes. Therefore this node is ON when [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] OR [[ErbB2_ErbB4/Epithelial|ErbB2_ErbB4]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]] OR [[ErbB4_ErbB4/Epithelial|ErbB4_ErbB4]] is ON.\n\n

ErbB4_Y1242 (Tyr_1242 site of ErbB4) is activated upon receptor dimerization [1].\n\n

S_34 1 S_214 1 S_220 1 S_20 1

ErbB2_Y1221_22 (Tyr_1221/22 site of ErbB2) is activated when ErbB2 dimerizes with [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] [1].\n\n

ErbB2_Y1221_22 (Tyr_1221/22 site of ErbB2) is activated upon receptor dimerization [1].\n\n

ErbB2_Y1221_22 (Tyr_1221/22 site of ErbB2) is activated upon receptor dimerization [1].\n

S_195 1 S_220 1 S_91 1

EGFR_Y1068 (Tyr_1068 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer). This site can also be activated (phosphorylated) by Src when Integrins AND Cas AND EGFR_Free are active.\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [3, 1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [3, 1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

S_194 1 S_195 1 S_99 1 S_214 1 S_157 1 S_52 1

PTP1b is active unless regulated by EGFR bound to its ligand {[1]}, or stress {[2]}. Regarding EGFR: all dimers of EGFR (EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4) will be positive regulators. Furthermore, because EGFR signaling continues while EGFR is being internalized [7], the following localizations of EGFR will also be regulators of PTP1b: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, and EGFR_EGFR_TGFa_CCV. \n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*EGFR bound to its ligand inactivates PTP1b {[1]-all}. Because it is not clear which site on EGFR PTP1b binds to, the upstream regulators of PTP1b are all activated (ligand-bound) dimer and localization versions of EGFR (listed below). (Note that EGFR_EGFR_TGFa_End is left out. This is because TGFa dissociates from the receptor once the complex enters the endosome. This is the opposite of what happens with EGF_bound EGFR which remains as one complex with the ligand.) Once more detail on the binding site of PTP1b is found, these EGFR regulators will be replaced with regulators denoting specific binding sites.\n<br>*PTP regulated by EGFR? {[4]}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*H2O2 inhibits PTP1b {[2]-p(1059)}\n

S_99 1 S_214 1 S_194 1 S_52 1 S_157 1 S_227 1 S_66 1 S_86 1 S_195 1 S_30 1 S_16 1 S_174 1 S_29 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_86 1

*Src can phosphorylate Cbl_RTK, which activates it {[6], p. 911}.\n<br>*When Src phosphorylates Cbl_RTK AND there is activated Cdc42/Cool/Pix, it becomes sequestered from EGFR and EGFR becomes very stable (which can even cause transformation). so this is a negative input to Cbl_RTK {[5], p. 33}.\n<br>*Src is constitutively associated with Cbl_RTK {[6], p. 915}.\n<br>*Cbl_RTK is localized to FA's when Src AND Cdc42 are active, so Src+Cdc42 is a negative input to Cbl_RTK. {[6], p. 915}.\n<br>*When Src phosphorylates Cbl_RTK, it allows PI3K, to associate with Cbl {[6], p. 915}.\n\n

*When Grb2 is activated (associated with EGFR), it can attract (activate) Cbl_RTK {[6], p. 908}{[4], p. 687}\n<br>*Grab2 mediates the binding of EGFR to the E3 ubiquitin ligase c-Cbl to start the cascade of events leading to internalization and degradation. {[1], p.745}\n<br>*Cbl binding to EGFR via Grb2 is necessary for receptor internalization. {[2]-p.566}\n\n

*Phosphorylation of EGFR on Thr 654 by PKC leads to inhibition of Cbl recruitment to EGFR and the receptor's subsequent ubiquitination. [3] (See more notes in the Notes and Thoughts section below)\n<br>*PKC can phosphorylate EGFR on Thr_654 following EGFR stimulation which blocks/lowers Cbl_RTK's ability to bind to the EGFR {[5], p. 29}.\n\n

*Cbl can bind EGFR directly either directly by binding to phosphorylated Y1045, or indirectly via Grb2 {[2], p.566}. \n<br>*When EGFR is autophosphorylated (active), it can attract (activate) Cbl_RTK {[6], p. 908}.\n<br>*If EGFR is Tyr_phosphorylated at a low level, it can have activity but not be able to attract Cbl_RTK for negative regulation {[6], p. 910}{[2], p.566}.\n<br>*Cbl is activated by activated EGFR {[7], p.183}.\n\n

*Spry2 can bind directly to Cbl_RTK AND CIN85 which prevents CIN85-mediated clustering of Cbl_RTK, which is required for EGFR ubiquinylation and downregulation {[5], p. 29}{[4], p. 689}.\n<br>*When Spry2 is in the membrane, it can become phosphorylated and then it looks like phosphorylated EGFR, so Cbl_RTK is sequestered and negatively regulated. This is CIN85-dependent {[6], p. 913}.\n<br>*Spry2 down regulates Cbl {[6], p. 910}.\n\n

S_19 1 S_244 1 S_149 1 S_105 1 S_110 1 S_184 1 S_244 1 S_149 1 S_105 1 S_110 1

Rho is a positive regulator [9, 3, 2, 8].\n\n

*Rho is an upstream of RhoK {[6]-p(761)}\n<br>*RhoK is directly effected by Rho. {[3]-p(2); [2]-p(62)}\n<br>*RhoK is an effector of RhoA {[4]-p(7840)}\n<br>*RhoK is a downstream effector of Rho {[5]-p(16919)}\n<br>*RhoK is directly activated by Rho {[9]-p(3); [8]-p(274)}\n

S_228 1

S_84 1 S_240 1 S_240 1 S_84 1 S_128 1 S_128 1 S_240 1

Cas [6, 2] OR EGFR [4, 1] can activate Nck. Thus all dimers of EGFR (EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4) will be positive regulators. Furthermore, because EGFR signaling continues while EGFR is being internalized [5], the following localizations of EGFR will also be regulators of Nck: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Phosphorylation of Cas by FAK can result in the recruitment of Crk and Nck adaptor proteins {[6]-p.12,[2]-p.1}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Nck2 can bind EGFR through its its SH2 domain {[1]-p(2329)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_227 1 S_194 1 S_99 1 S_29 1 S_16 1 S_214 1 S_66 1 S_52 1 S_129 1 S_174 1 S_195 1 S_139 1 S_157 1 S_30 1

RalBP1 is activated by Ral [3, 4, 2, 8]. \n\n

*RalBP1 is activated by Ral {[3]-p(162), Fig. 4, [4]-p(164)} \n<br>*Ral when active interacts with RalBP1 {[7]-p(8)} \n<br>*RalBP1 is effected by Ral, and contains a RhoGap domain that is active towards Cdc42 and Rac1 {[6]-p(4)} \n<br>*RalBP1 is downstream of Ral {[2]-p(9), [8]-p(3, 4)} \n\n

S_112 1

Gbg_12_13 is an idealized Gbg that specifically binds Ga_12_13. Gbg_12_13 is activated by the GPCR alpha-12_13_R when it is associated with Ga12_13 (i.e., when both Ga_12_13 and Gbg_12_13 are OFF). It is deactivated when Ga_12_13 is GDP-bound (OFF) unless they are both OFF and alpha-12_13_R is ON. If Ga_12_13 is ON, then Gbg_12_13 is separated and is ON. {[8, 1, 9, 6, 7, 3, 2]}\n\n

S_213 1 S_197 1 S_89 1 S_197 1

Inactive Rho is a negative regulator[2]. Src OR Fer OR EGFR are positive regulators [6, 7, 5, 8]. Thus all dimers of EGFR (EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4) will be positive regulators. Furthermore, because EGFR signaling continues while EGFR is being internalized [3], the following localizations of EGFR will also be regulators of p120_catenin: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End. The positive regulators are made dominant to the negative regulation.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*p120 can be phosphorylated by several kinases such as Src in response to growth factors {[6]-p.14} \n<br>*p120_catenin is a substrate for Src {[7]-p.662}{[4]-p.9}\n<br>*p120_catenin is phosphorylated by Src, which increases its binding affinity for E-cadherin {[5]}{<cite>Piedra</cite>-p.2287} \n\n

*see EGFR_EGFR_EGF_PM above.\n

*Inactive Rho can sequester p120 catenin which gets released upon the activation of Rho {[2]-p.449}\n\n

*Fer kinase constitutively binds to p120_catenin. Upon its activation it phosphorylates p120 which (at least in vitro) increases its ability to bind to [[E-cadherin]] {[8]-p.49,50}.\n\n

*EGFR is suggested to, independently of Src, either directly or indirectly via non-Src family kinases phosphorylate p120_catenin at Y228 {[8]-p.50}.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_139 1 S_30 1 S_157 1 S_244 1 S_194 1 S_227 1 S_66 1 S_214 1 S_228 1 S_58 1 S_99 1 S_52 1 S_29 1 S_16 1 S_195 1 S_174 1

This node represents the ErbB2:ErbB3 heterodimer. It is activated by NRG AND ErbB2_Free AND ErbB3_Free. Pertuzumab blocks the formation of the dimer (and hence the activation of the complex). ErbB2_Lysosome represents ErbB2_ErbB3 being degraded in lysosome, and deactivates ErbB2_ErbB3 (only if it was previously active). The previous activation state of ErbB2_ErbB3 is important not only for the more realistic effects of the negative regulators, but also to represent the recycling of the receptor complex in the absence of the inhibitors; i.e., if ErbB2_ErbB3 is activated with no negative regulators around, it will keep "recycling" and remain active, until an inhibitor turns it off.\n\n

*Neurogulins interact with ErbB3. [11]\n<br>*Neuregulins induce the formation of ErbB2_ErbB3 and ErbB2_ErbB4. [13]\n\n

*This species represents the ErbB2_ErbB3 complex being degraded in lososome. Currently this is the only negative regulatory mechanism of ErbB2_ErbB3 (except for drugs).\n

*Monoclonal antibody to prevent ErbB2 dimerization; a dominant negative regulator [15].\n\n

Because ErbB2 doesn't seem to undergo endocytic downregulation [9], the EGFR_ErbB2 complex will remain active once activated. The only negative regulation of ErbB2 complexes will be limited to the antibody Trastuzumab (until more is known about negative regulation of ErbB2).\n\n

ErbB2_ErbB3 is activated by ErbB2_Free, which represents inactive ErbB2 on the cell surface.\n\n

ErbB2_ErbB3 is activated by ErbB3_Free, which represents unliganded ErbB3 on the cell surface.\n\n

S_91 1 S_92 1 S_91 1 S_107 1 S_117 1 S_31 1 S_162 1 S_92 1 S_91 1

S_91 1 S_50 1 S_35 1 S_50 1

ESCRT_II is activated by ESCRT_I.\n\n

*Hrs (ESCRT_0) mediates the recruitment of ESCRT_I to endosomal membranes by binding to TSG101 in the ESCRT-1 complex.{[4]-p(644)} \n<br>*ESCRT_I recruits the ESCRT_II complex.{[5]-p(351)}\n

S_15 1

Rap1 is activated by cAMP [16, 17, 9, 3, 11, 4, 13], and the ability of cAMP to activate Rap1 has been shown to require Src AND PKA [2, 14]. Thus, cAMP, Src, and {PKA OR CaMK} are in a three-way AND. CaMK is OR with PKA because they phosphorylate the same site [10]. This may also explain why PKA is not necessary to activate Rap1 [3]. Gai is a negative regulator of Rap1 through RapGAP [6, 8] which is not included in the network. Since the negative regulation is through GAP activity, Gai will be dominant and turn Rap1 OFF only when Rap1 is ON.\n\n

*Rap1b activated by Src through C3G and by cAMP {[16]-p.89(248), Fig. 9}\n<br>*PKA phosphorylates Src at serine 17 which activates Src to activate Rap1. {[3]-p(3)}\n

*CaMKIV can phosphorylate the small GTP-binding Rap1b in vitro, perhaps at the site phosphorylated by PKA {[10]-p(4)}\n\n

*Rap1b is directly activated by cAMP {[16]-p.1(241)}\n<br>*Rap1b activated by Src through C3G (a GEF) and by cAMP (through EPAC, another GEF) {[16]-p.89(248), Fig. 9}\n<br>*Rap1 is acitvated by cAMP {[17]-p(4); [9]-p(1)}\n<br>*The ability of cAMP to activate Rap1 in selected cells has recently been shown to require Src and PKA {[2]-p(2); [14]-p(2)}\n<br>*Rap1 is activated by cAMP {[3]-p(1); [11]-p(294), Fig. 3; [4]-p(1638)}\n<br>*Members of the Rap-directed family of GEFs are regulated by cAMP, and are thus subject to regulation through G-protein activation of AC. \n<br>*cAMP can activate Rap1 independently of PKA {[13]}\n

*Phosphorylation of Rap1B at serine 179 by PKA has been proposed to be a key step in Rap1b activation {[16]-p.2(242)}\n<br>*PKA phosphorylates Rap1b {[10]-p(4)}\n<br>*PKA activation of Rap1b has been proposed to result from the direct phosphorylation by PKA on the Src tyrosine kinase {[2]-p(1)}\n<br>*Rap1 is activated by PKA {[3]-p(2); [11]-p(294), Fig. 3}\n<br>*PKA can directly phosphorylate Rap1 {[3]-p(3)}\n<br>*PKA phosphorylates Rap1, which not only blocks c-Raf activation, but also binds b-Raf, resulting in b-Raf activation. {[12]-p(2)}\n\n

S_68 1 S_94 1 S_201 1 S_244 1 S_188 1 S_133 1 S_244 1 S_188 1 S_94 1 S_201 1

B_Arrestin is activated by GPCR's when they are phosphorylated by GRK [4, 3, 1, 2]. Therefore, Palpha-s_R OR Palpha-q_R OR Palpha-i_R OR Palpha-12_13_R need to be ON to activate B_Arrestin (for Palpha-s_R see alpha-s_R...).\n\n

S_141 1 S_169 1 S_231 1 S_179 1

TAO_1_2 is activated by stress {[1]-all}\n\n

TAO_1_2 is activated by stress. {[1]-all}

S_86 1

IP3R is activated by several pathways. IP3 binding in the presence of Ca activates IP3R [17, 20, 4, 12, 2, 9, 11, 5, 7, 13, 19, 18, 8, 6, 3]. PKC phosphorylates IP3R increasing the affinity of IP3 binding to IP3R, and therefore is not suffucient or required for any activity regulation, and will fall out of the logic [3].\nIP3R can be also activated by phosphorylation by PKA [6] OR binding of Gbg_i [10, 14].\nThe inactivation of IP3R is conducted when Ca AND CAM are present [6, 3]. IP3R can also be inactivated when Ca is present without IP3 [3].\nPP2A is a negative regulator that is dominant to PKA when IP3R is active due to PKA phosphorylation [6].\n\n

*Calmodulin mediates Ca-dependent inhibition of IP3R function {[6]-p(443)}\n<br>*IP3R is autophosphorylated at the same sites used by PKC and PKA {[6]-p(445)}\n<br>*CaM inhibited the IP3-induced activity only in presence of high cytosolic Ca concentrations. CaM shifted the inhibitory part of the Ca response curve towards lower Ca concentrations and makes the bell-shaped curve steeper. {[3]-p(23)}\n<br>*CaM inhibits IP3 binding in a Ca-independent way. {<cite>Kasri</cite>-p(24)}\n\n

*PP2A can deactivate IP3R (Ca). {[6]-p(444)}\n\n\n

*PKA can activate IP3R (Ca). {[6]-p(444)}\n\n

*Ca initially released by IP3R feeds back to augument further Ca release in a positive manner. Higher concentration inhibit channel function, creating the classical oscillatory pattern of Ca release observed in response to most agonist-mediated pathways {[6]-p(443), [3]-p(20)}\n<br>*Ca without IP3 inhibits IP3R [3]\n<br>*For IP3R1 and -3, Ca inhibits IP3R when the levels of IP3 lower {[3]-p(20)}\n<br>*Ca AND IP3 activate IP3R {[6], [3]-p(20)}\n\n

*Ca is a downstream pathway from IP3 {[17]-p(5), Fig.3}\n<br>*IP3 promotes release of Ca from intracellular stores {[20]-p.2(282), [4]-(p(3), Fig.2), [12]-p(502), [2]-p(6), [9]-p(1), [11]-p(340)}\n<br>*Ca is downstream of IP3 {[5]-p(534)}\n<br>*IP3 causes the release of Ca from ER {[7]-p(260), [13]-p(1), [19]-p(1)}\n<br>*Ca is produced by IP3 {[18]-p(1)}\n<br>*IP3 induces mobilization of Ca from intracellular Calcium stores. {[8]-p(968)}\n\n

S_111 1 S_229 1 S_229 1 S_98 1 S_111 1 S_3 1 S_229 1 S_98 1 S_133 1 S_43 1 S_98 1 S_229 1 S_98 1 S_111 1 S_3 1 S_229 1 S_98 1 S_222 1 S_98 1 S_3 1 S_222 1 S_43 1 S_133 1 S_229 1 S_111 1 S_229 1 S_98 1 S_111 1 S_3 1 S_229 1 S_98 1

This node represents the EGFR:ErbB3 heterodimer. It is activated by EGF AND EGFR_Free (representation of an inactive EGFR) AND ErbB3_Free (representation of an inactive ErbB3) AND NRG, unless EGFR_T654 is active. Due to the hierarchy in the activation of the various ErbB's, the activation of EGFR_ErbB3 occurs only when ErbB2_Free is not present.\n\n

*Neurogulins promote ErbB1:ErbB3 heterdimers [] (Although this is true for the beta isoform only, our NRG represents both isoforms and hence NRG will be an activator of the complex. [])\n\n

*(Our EGF represents both EGF that is specific to EGFR and EGF_like ligands that result in the activation of the EGFR:ErbB2 homodimer)\n<br>*EGF activates EGFR {[3]-p(3), [14]-p(1), []-p(4-Fig. 2), [10]-p(1), []-p(1), []-p(2-Fig. 1)}\n<br>*EGFR autophosphorylates at five known tyrosine residues after the addition of EGF {[14]-p(2)}\n<br>*EGF is known to activate EGFR {[7]-p(3)} \n<br>*EGF binds EGFR {[1], <cite>Schoeberl</cite>-p(1)}\n<br>*EGF binds to EGFR which causes dimerization and subsequent cross-phospohrylation of specific residues in the C-terminal tail of the partnering receptor{[1], <cite>Schoeberl</cite>-p(564)}\n\n

EGFR_ErbB3 is activated by EGFR_Free, which represents unliganded EGFR on the cell surface.\n\n

*ErbB2 is the preferred dimerizing partner for all ErbBs [] ; Hence ErbB2_Free will be a negative regulator of other dimers.\n\n

EGFR_ErbB3 is activated by ErbB3_Free, which represents inactive ErbB3 on the cell surface.\n\n

S_114 1 S_31 1 S_149 1 S_41 1 S_107 1 S_117 1

MKK7 [10, 32, 4, 33, 12, 17, 28, 9, 20, 31, 19, 15, 21] OR SEK1 [8, 32, 24, 33, 29, 12, 10, 4, 22, 31, 17, 6, 19, 11, 21, 9, 20, 11, 13, 28, 34] activate SAPK when its inactive.\r\nSAPK is deactivated by PP2A [14, 17, 2] OR MKPs [32, 17, 27, 31] when SAPK is ON. They are made dominant.\r\n\r\n

*PP2A can dephosphorylate MEK1 and ERK-family kinases {[14]-p(3),[17]-p(2)}\r\n<br>*PP2A negatively regulates SAPK {[2]-p(4)}\r\n\r\n

*SAPK(JNK) is activated by MKK4/7 {[10]-p(3), Fig. 1, [32]-p(3), [4]-p(665-Fig. 1)}\n<br>*SAPK activated by MKK7. {[33]-p(822), [12]-p(2-Fig. 1)}\n<br>*SAPK is activated and phosphorylated by MKK7 {[17]-p(1), [28]-p(187, Fig. 1)}\n<br>*SEK1 and MKK7 phosphorylate JNK on Thr183 and Tyr185 and activate it {[9]-p(1), [20]-p(240)}\n<br>*SAPK is regulated and phosphorylated by MKK7 {[31]-p(66)}\n<br>*MKK7 is a dual specificity kinase that phosphorylates JNK {[19]-p(2), [15]-p(661)}\n<br>*MKK7 and MKK4 is a direct upstream of SAPK {[21]-p(3)}\n\n

*MKP terminates the activity of SAPK and p38 by their dephosphorylation {[32]-p(6)} \n<br>*MKP-1 inactivates SAPK {[17]-p(2)}\n<br>*MKP-3 is Erk-specific. It cannot dephosphorylate p38 or SAPK {[27]-p(3)}\n<br>*MKPs 1, 2 and 4 inactivate Erk, p38, and SAPK {[31]-p(76, 78)}\n

*Sek1 activates SAPK {[8]-p(342), [32]-p(3), [24]-p(30, Fig. 1), [33]-p(822), [29]-p(1), [12]-p(2-Fig. 1), [10]-p(3), Fig. 1, [4]-p(665-Fig. 1)}\n<br>*Sek phosphorylates SAPK {[22]-p(375), [31]-p(66)}\n<br>*Sek1 activates and phosphorylates SAPK {[17]-p(1), [6]-p(2)}\n<br>*MKK4 is a dual specificity kinase that phosphorylates JNK {[19]-p(2)}\n<br>*MKK4 can activate both p38 and JNK {[19]-p(4), [11]-p(2)}\n<br>*MKK7 and MKK4 is a direct upstream of SAPK {[21]-p(3)}\n<br>*SEK1(MKK4) and MKK7 phosphorylate JNK on Thr183 and Tyr185 and activate it {[9]-p(1), [20]-p(240), [11]-p(2)}\n<br>*MKK4 and MKK7 phosphorylate and activate JNK {[13]-p(2), [28]-p(187-Fig. 1), [34]-p(323)}\n<br>*Dominant negative MKK$ inhibits SAPK.\n\n

S_59 1 S_147 1 S_100 1 S_43 1 S_100 1 S_226 1 S_147 1 S_100 1 S_43 1 S_100 1

ErbB3_Y1180 (Tyr_1180 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1180 (Tyr_1180 site of ErbB3) is activated upon receptor dimerization [].\n\n

S_91 1 S_20 1 S_99 1

ESCRT_III is activated by ESCRT_II OR ESCRT_I.\n\n

*ESCRT_II instigates the formation of ESCRT_III complex.{[5]-p(351)}\n<br>*ESCRT_II recruits ESCRT_III.{[]-p(644)} \n\n

*ESCRT_I facilitates recruitment of ESCRT_II and ESCRT_III.{[4]-p(689)}\n\n\n

S_15 1 S_93 1

IP3_345 [14, 25, 23, 73, 54, 63, 75, 55, 62, 16, 46, 68, 7, 61, 67, 3, 47, 53, 69, 26, 28, 35, 72, 30] OR PIP2_34 localizes Akt to the membrane [26, 30, 53, 14, 71, 57, 16, 9, 47, 69, 8, 64, 30].\nAfter Akt becomes localized at the membrane PDK1 must phosphorylate Akt for it to become active [10, 71, 15, 12, 47, 26, 25, 64, 38, 19, 43, 20, 57, 44, 16, 9, 5, 58, 31, 14, 48, 55, 54, 59, 61, 76, 69, 4, 13, 2, 74, 60, 35, 62, 40, 49, 30], but only if Akt was OFF [62]. Alternatively, CamKK can do that phosphorylation [26, 32, 76], so CamKK and PDK1 are in an OR.\nFinally, ILK [14, 20, 42, 61, 31, 65, 21, 1] AND Src [52] are required for Akt activation.\nPP2A inhibits Akt by dephosphorylation [57, 12, 6, 35, 61, 47, 66, 40, 18], but only if Akt is already ON [18, 40]\n\n

*Akt is phosphorylated by PDK1 on Thr308 in its activation loop {[10]-p(6), [71]-p(260), [15]-p(2), [12]-p(5), [47]-p(7), [26]-p(977, 980, 988), [25]-p(2), [64]-p(2)}\n<br>*Akt is a downstream of PI3K and activated by PDK1 {[38]-p(5)}\n<br>*Akt is activated by PDK1 {[19]-p(2, Fig.1), [43]-p(41, Fig.6), [20]-p(2, Fig.1), [57]-p(2), [44]-p(103, Fig.2), [16]-p(1), [9]-p(245), [5]-p(5972)</cite>}\n<br>*PDK1 phosphorylates and activates Akt in vitro. {[58]-p(6)}\n<br>*Akt is activated by PDK1 and ILK {[31]-p(1)}\n<br>*Akt becomes fully activated upon phosphorylation of the regulatory site by PDK1 {[14]-p(7), [48]-p(2)}\n<br>*PIP3_345 and PIP2_34 recruit Akt and PDK1 to plasma membrane, where PDK1 phosphorylates and activates Akt {[16]-p(1), [55]-p(1), [54]-p(3)}\n<br>*PDK1 mediates the phosphorylation (activation) of Akt as well as S6K {[59]-p(2)}\n<br>*PDK1 activates one of the two sites on Akt that are required for its full activation {[61]-p(1)}\n<br>*PDK1 efficiently phosphorylates Akt at Thr_308 and overexpression of PDK-1 is sufficient to activate Akt in transfected cells and the binding of PIP3-345 to Akt PH domain is reqired for PDK-1 to phosphorylate Akt {[76]-p(2908, 2909)}\n<br>*PDK-1 fully and efficiently activates Akt at Thr308 {[69]-p(767, 769)}\n<br>*PDK1 phosphorylates AKt on Thr308 {[4]-p(1254, Fig.5), [13]-p(193, 195), [2]-p(214}\n<br>*PDK1 phosphorylates AKt on Thr308 in a PIP2_34/PIP3_345 dependent manner. {[74]-p(7), [30]-p(161, 162)}\n<br>*PDK1 can phosphorylate the activation loop of Akt (Thr308 in PKBa) in the presence of PIP3. And Akt is the only substrance of PDK1 that requires the presence of PIP3 to be efficiently phosphorylated by PDK1. {[60]-p(6, 8-Fig. 1), [30]-p(161,162)}\n<br>*Overexpression of PDK1 induced phosphorylation of Akt on Thr308 and Ser473. {[58]-p(7)}\n<br>*After Akt is recruited to the membrane by PIP3_345, it is activated by phosphorylation on Thr308 and Ser473 by PDK1 and Ser473 kinase, respectively. {[35]-p(4)}\n<br>*P90RSK, p70S6K and Akt are activated with different temporal regulations while some substrates are phosphorylated by PDK1 constitutively {[62]-p(1)}\n<br>*PDK1 phosphorylates and activates Akt, PKC and p70S6K {[40]-p(8)}\n<br>*PDK1 is crucial for activation of Akt. {[49]-p(1)}\n<br>*PDK1 regulates Akt. {[49]-p(2)}\n\n

*ILK can directly phosphorylate PKB {[14]-p(7)}\n<br>*ILK activates Akt {[20]-p(2, Fig.1)}\n<br>*Upon stimulation by PIP3_345, ILK catalyzes serine/threonine phosphorylation of Akt {[42]-p(2), [33]-p(8)}\n<br>*ILK phosphorylates Akt on Ser473 and GSK3 {[61]-p(4)}\n<br>*Akt is activated by PDK1 and ILK {[31]-p(1)}\n<br>*ILK stimulates the phosphorylation of AKT, GSK3, and both PDK1 and Akt have been shown to associate with ILK {[65]-p(3)}\n<br>*ILK can phosphorylate AKT at Ser473 {[21]-p(568, Fig.1, Table 2), [1]-p(2328)}\n\n

*Akt is inactivated by PP2A {[57]-p(2), [12]-p(3), [6]-p(428), [35]-p(2, Fig.1)}\n<br>*PTEN decreases the level of PIP3 and prevents Akt activation, but the inactivation occurs via dephosphorylation by PP2A {[61]-p(4)}\n<br>*PP2A can dephosphorylate and inactivate Akt {[47]-p(1)}\n<br>*PP2A dephosphorylates both sites and inactivates Akt {[47]-p(8)}\n<br>*Integrin a2b1 regulates Akt via PP2A {[66]-p(3)}\n<br>*Akt is directly inactivated, following dephosphorylation by PP2A {[40]-p(9)}\n<br>*Activated Akt is inactivated (dephosphorylated) by PP2A {[18]-p(1, 2, 4)}\n\n

*Akt is inactivated by PIP3_345 {[26]-p(999)}\n<br>*PIP3_345 recruits Akt to the membrane {[14]-p(1), [25]-p(2), [23]-p(357)}\n<br>*Akt binds pip3_345 and PIP2_34 {[14]-p(7)}\n<br>*PDK1 binds pip3_345 and PIP2_34 which causes the recruitment of Akt to the plasma membrane and co-localize it with a constitutively active kinase kinase,PDK1. Also they allow formational change in Akt that allows it to be phosphorylated by PDK1 {[57]-p(2), [54]-p(3)}\n<br>*PIP3_345 recruits Akt and PDK1 to plasma membrane, where PDK1 phosphorylates and activates Akt {[63]-p(1), [75]-p(2), [55]-p(1), <cite<Biondi</cite>-p(2)}\n<br>*PIP3_345 and PIP2_34 recruit Akt and PDK1 to plasma membrane, where PDK1 phosphorylates and activates Akt {[16]-p(1), [46]-p(3)}\n<br>*Reducing PIP3_345 suppresses Akt phosphorylation/activation {[68]-p(1174), Fig. 2}\n<br>*PIP3_345 binds directly to Akt {[7]-p(1)}\n<br>*Akt is activated downstream of PI3K requiring PIP3_345 {[61]-p(1)}\n<br>*Inactivation of PTEN leads to constitutive activation of PI3K-Akt pathway {[67]-p(3)}\n<br>*PIP3_345 recruits and activates Akt and PDK1 {[3]-p(1)}\n<br>*Akt is activated via PIP3_345 and PIP2_34. {[47]-p(7), [53]-p(3)}\n<br>*Akt is a target for PIP3_345 {[69]-p(767)}\n<br>*Akt is activated by PIP3_345 and PIP2_34 [26]\n<br>*PDK1 can phosphorylate the activation loop of Akt (Thr308 in PKBa) in the presence of PIP3. And Akt is the only substrance of PDK1 that requires the presence of PIP3 to be efficiently phosphorylated by PDK1. {[60]-p(6, 8-Fig.1), [30]-p(161, 162)}\n<br>*upon growth factor stimulation, binding of Akt to PIP3 mediates translocation of Akt to the plasma membrane, and renders the kinase accessible to upstream kinases such as PDK1 and Src. {[52]-p(1)}\n<br>*Akt translocates to the plasma membrane through binding to PIP3 generated by PI3K, where Act meets with Src. {[52]-p(2)} \n<br>*Akt binds pip3_345 and is translocated to the plasma membrane {[28]-p(1), [35]-p(4)}\n<br>*PI3K activation by growth factors results in an increase in PIP3_345, which leads to the translocation of Akt to the membrane, which allows PDK1 to phosphorylate Thr and Ser on Akt. {[14]-p(29,32),[24],<cite> Kaay</cite>}\n<br>*PI3K activated Akt involving binding of PIP3_345 to its PH domain. {[27]-p(1458)}\n<br>*Akt is directly activated by PIP3_345 {[54]-p(3)}\n<br>*The N-terminal PH domain allows Akt directly bind to PIP3_345 and PIP2_34 {[64]-p(1)}\n<br>*PIP3_345 facilitates the activation of Akt {[72]-p(5)}\n\n

*PIP2_34 and PIP3_345 play a crucial role in activation of Akt {[10]-p(6), [53]-p(3)}\n<br>*Akt binds pip3_345 and PIP2_34 {[14]-p(7)}\n<br>*Akt is also activated by binding to products of PI3K, PIP and PIP2 {[71]-p(260)}\n<br>*PDK1 binds pip3_345 and PIP2_34 which causes the recruitment of Akt to the plasma membrane and co-localize it with a constitutively active kinase kinase,PDK1. Also they allow formational change in Akt that allows it to be phosphorylated by PDK1 {[57]-p(2)}\n<br>*PIP3_345 and PIP2_34 recruit Akt and PDK1 to plasma membrane, where PDK1 phosphorylates and activates Akt {[16]-p(1)}\n<br>*Akt is activated in part by direct interaction of PIP2_34 with its PH domain {[9]-p(245), [47]-p(7)}\n<br>*PIP2_34 is binding to Akt induces a small (3-5 fold) but reproducible activation of Akt {[69]-p(767, 769)}\n<br>*Akt is activated by PIP3_345 and PIP2_34 {[26]-p(975, 978, 979)}\n<br>*PI(3,4)P2 can activate AKT. {[8]-p(1)}\n<br>*The N-terminal PH domain allows Akt directly bind to PIP3_345 and PIP2_34 {[64]-p(1)}\n

S_128 1 S_103 1 S_244 1 S_217 1 S_74 1 S_54 1 S_223 1 S_103 1 S_74 1 S_54 1 S_244 1 S_217 1 S_103 1 S_43 1

ErbB3_Y1241 (Tyr_1241 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1241 (Tyr_1241 site of ErbB3) is activated upon receptor dimerization [].\n\n

S_20 1 S_99 1 S_91 1

tion Mechanism==\nCIN85 is activated by Cbl (specifically Cbl_RTK - see [[Cbl]]) [7].\n\n

S_81 1

PI5K is activated by RhoK [18, 7, 32, 8, 29, 15, 4, 22, 6, 28], PA [15, 29, 16, 9, 34, 10, 19, 38, 18, 33, 37, 36, 28], and ARF [16, 5, 33, 34, 3, 38, 2, 36, 18, 28]. They all can activate PI5K independently [18], so they are in an OR relation.\nWhen PI5K is OFF and talin is OFF, then Src AND Fak can activate PI5K [35, 32, 27, 30, 11, 13, 18, 28]. When PI5K is ON and talin is ON, PI5K is localized to focal adhesions and ON [11, 13, 13, 24, 23, 14, 21, 35, 12, 26, 39, 18].\nThere is evidence that integrin and PI5K binding to talin is mutually exclusive, but it is not clear if this is the case [17]. We have not made it so in order to have PI5K localized to focal adhesions. \n\n

*PI5K is activated by Src {[32]-p(284)}\n<br>*[PIPKIg90] Src phosphorylates PIPKIg90 on the tail (the tail that distinguishes it from PIPKIg87) which stimulates binding of PIPKIg90 to talin. {[27]-all}\n<br>*[PIPKIg90] The phosphorylation by Src also may enchace the activation by Fak. {[30]-p(790)}\n<br>*[PIPKIg90] Unlike in {[27]}, Src was not found to be a positive regulator of PIPKIg90-talin interaction. However, Src phosphorylation does inhibit the negative phosphorylation by Cdk5, so Src is indirectly positive. {[30]-p(797)}\n\n

*Talin recruits the PIP2-synthesizing enzyme PIPKIb to dadhesions. {[11]-p(97), Fig. 1}\n<br>*one PIP5K splice sioform localizes to focla adhesions by binding talin and this interaction stimulates its activity {[13]-p(577)}\n<br>*Talin binds to and activates PIP2 producer PIPKIg-90. In turn, PIP2 enhances talin-integrin interactions. However PIPKI90 competes with integrin b tails for the sites of talin. {[24]-p(3)} (=> If talin activates PIPKI90, it doesn't activate integrins) \n<br>*PIP2_45 binds to Talin to induce its association with integrin b1 tails. Notably, Talin binds to and activates one splice varient of the PIP2_45-producing enzyme - PIPKIj-90. Therefore, talin can stimulate PIP2_45 production that in turn enhances talin-integrin interactions.{[23]-p(6)}\n<br>*Talin also binds to and activates PIPKI90 which produces PIP2_45 {[14]-p(432)}\n<br>*PIPKI90 and integrins compete for the binding site in talin {[14]-p(432), [21]-p(28890)} \n<br>*Integrin signalling via FAK and Src promotes binding of talin to a PIP kinase. Complex formation activates a PIP kinase and protmotes translocation of talin to the plasma membrane, although the latter is independent of kinase activity. {[35]-p(832)}\n<br>*Since binding to integrins and PIP kinase is mutually exlusive, it is unclear whether the displacement of PIP kinase is required {[35]-p(832)} \n<br>*"PIPKIg-90 localizes to sites of integrin-mediated adhesion, and talin vinding activates PIPKIg-90, which catalyzes the production of PIP2_45. PIP2_45 binds to talin and induces a conformational change that enhances talin association with integrin beta tails... However, by competing with integrin tails for binding to talin, PIPKIg-90 probably plays both positive and negative roles in integrin regulation. This activity is probably caused by Src, acting downstream of focal adhesion kinase, because Src-mediated tyrosine phosphorylation of PIPKg-90 greatly increases its affinity for talin resulting in a more effective displacement of integrin tails from talin" {[21]-p(28894)} \n<br>*Talin binds and activates PIPKIg {[26]-p(695), [12]-p(87)} \n<br>*PIPKIg is recruited to FA through binding to talin. This binding increases the activity of PIPKIg, resulting in production of more PIP2_45, which then regulates talin, vinc, and other FA proteins. {[26]-p(697)} \n<br>*Talin-PIPKIg interaction is critical for FA {[12]-p(88), [39]-p(92)}\n<br>*[PIPKIg90] PIPKIg90 is specific for binding talin (PIPKIg87 does not). Talin recruits PIPKIg90 and activates it. {[30]-p(789)}\n<br>*PIP5K is targeted to focal adhesions by talin, and phosphorylation by FAK increases lipid kinase activity and binding to talin {[18]-p(90)}\n<br>*PIP5K is targeted to focal adhesions by talin, and phosphorylation by FAK increases lipid kinase activity and binding to talin {[18]-p(90, 92), [28]-p(86)}\n<br>*The recruitment and activation by talin appear critical for focal adhesion assembly, but additional factors such as small GTPases probably cooperate in this process {[18]-p(92)}\n\n

*FAK phosphorylates PIPKIg661, thereby stimulating its activity {[11]-p(96), Fig. 1}\n<br>*FAK can phosphorylate PIP5K and activate it. {[13]-p(577)}\n<br>*Tyrosine phosphorylation of PIP kinase by FAK has been reported to increase its affinity to talin and SHP2 can work as a phosphatase to weaken the links. {[31]-p(31208)}\n<br>*PIP5K is targeted to focal adhesions by talin, and phosphorylation by FAK increases lipid kinase activity and binding to talin {[18]-p(90, 92)}\n\n

*PI5K is stimulated by PA {[15]-p(237), [29]-p(498), [18]-p(88)}\n<br>*PI5K is activated by PA {[16]-p(2), [9]-p(4), [34]-p(1), [10]-p(3), [19]-p(6), [38]-p(241)}\n<br>*PI5K is regulated by both PA nad ARF {[33]-p(5), [34]-p(1, 2), [28]-p(83)}\n<br>*Type I PI4P5Ks can be stimulated in vitro by the PA {[38]-p(236)}\n<br>*PI5K is dramaticlly activated by PA {[37]-p(1303)}\n<br>*[PIPKIa] PA and ARF6 are both required for the activation of PIPKIa {[36]-p(528), all}\n<br>*PIPKI is regulated by G proteins, and by PA. PLD is required for FAs. {[39]-p(92)}\n<br>*Activation of PI5K is PA-dependent {[16]-p(3)}\n<br>*PLD is activated by ARF GTPases, and the activities of PLD and PIP5K can be amplified by reciprocal stimulation via their products PA and PIP2 {[18]-p(90-Fig. 2)}\n<br>*PA activates PI5K {[18]-p(94)} (Looks like it's sufficient)\n\n

*RhoA binds to PIP5K, and activation of PIP5K is done by RhoK {[18]-p(90), Fig. 2, [28]-p(83, 84)}\n<br>*PI5K is activated by Rho {[7]-p.3(3585), [32]-p(284)} \n<br>*Rho and Rac binds to PI5K, but it doesn't require GTP loading of Rho {[8]-p(2)}\n<br>*Rac and RhoA constitutively regulate PIP5K {[29]-p(498)}\n<br>*Rho stimulates PI5K activity in cell lysates {[15]-p(237)}\n<br>*Rho directly effects PI5K, which in turn produces, PIP2_45. {[4]-p(2)}\n<br>*all of PIP5K typeI isoforms are positively regulated by RhoA and Rac1, but also by Cdc42. The stimulation of PIP5K isoforms by RhoA is entirely mediated by RhoK, whereas the effects of Rac1 and Cdc42 are largely independent of the RhoA/RhoK relay. {[22]-p(7841)}\n<br>*PI5K is regulated by RhoA. {[6]-p(100)}\n<br>*The stimulation of PIP5K isoforms by RhoA is entirely mediated by RhoK {[18]-p(92)}\n<br>*PI5K binding to Rho GTPases is GTPases state independent. Binding of PI5K to Rac or Rho is specific and direct, but is not a trigger or prerequisite for kinase activation, but may serve as a recruitment of the kinase to specific compartments {[18]-p(93)} (Therefore Rho and Rac have no effect!!!!!!)\n\n

*Arf also activates PI5K {[16]-p(2), [5]-p(398)}\n<br>*PI5K is regulated by both PA nad ARF {[33]-p(5), [34]-p(4, 8)}\n<br>*ARF GTPases directly activate type I PIP5K enzymes {[3]-p(647)}\n<br>*In vitro, ARF1, ARF5 and ARF6 were all able to activate bacterial recombinant PI4P5K Ia in the presence of GTPgS and PA {[38]-p(234)}\n<br>*Arf6 is a direct activator of PIP5K responsible for generating PIP2. {[2]-p(3)}\n<br>*Interactions between ARF6 and PIP5K in PC12 cells were reported to be governed by a calcium-dependent mechanism involving the phosphorylation of the PIP5 Kinase. {[2]-p(3)}\n<br>*[PIPKIa] PA and ARF6 are both required for the activation of PIPKIa {[36]-p(528), all}\n<br>*Arf proteins under the influence of PIP2 stimulates PI5K producing more PIP2_45 {[16]-p(3)}\n<br>*Rac binds to and activates PIP5K. Bacterial uptake involves the recruitment by Rac to phagosome, and activation by ARF6. {[18]-p(90)}\n<br>*PIP5K is activated by ARF1 and ARF6 {[18]-p(90-Fig. 2)}\n<br>*ARF1, ARF6 activate PI5K in presence of PA. ARF6 colocalizes with PI5K in ruffling membranes {[18]-p(94)}\n<br>*To attain localized PIP2 synthesis, ARF6 and Rac collaborate -> Rac localizes PI5K to phagosomal cup and ARF6 controls its kinase activity {[18]-p(94)}\n\n

S_83 1 S_12 1 S_56 1 S_106 1 S_218 1 S_244 1 S_106 1 S_135 1 S_218 1

S_108 1 S_177 1 S_44 1 S_130 1 S_108 1

tion Mechanism==\nEGFR activates Spry2 [3]. Cbl is a negative regulator [2]. We are making the negative regulator dominant over the positive.\nBecause our model also accounts for EGFR dimers, EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4 will be all independent activators. Furthermore, because EGFR signaling continues while EGFR is being internalized [1], the following localizations of EGFR will also be regulators of Spry2: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*EGFR positively regulates Spry2 in two ways-- it phosphorylates it (which activates it directly), and it causes upregulation of its transcription, which counters the negative effect of Cbl's ubiquinization of Spry2 {[2], p. 29}, {[3], p. 911}.\n<br>*There is a feedback loop: EGFR_->Spry--|Cbl--|EGFR {[3], p. 911}.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*see EGFR_EGFR_EGF_PM above.\n<br>* Interesting question: what effects on EGFR internalization does GPCR_mediated transactivation of EGFR have?\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_227 1 S_81 1 S_139 1 S_81 1 S_99 1 S_81 1 S_52 1 S_81 1 S_29 1 S_81 1 S_195 1 S_81 1 S_157 1 S_81 1 S_16 1 S_81 1 S_30 1 S_81 1 S_174 1 S_81 1 S_194 1 S_81 1 S_214 1 S_81 1 S_66 1 S_81 1

Either PLC_g OR PLC_B can hydrolyze PIP2_45 to IP3; both are AND to PIP2_45 [5, 16, 7, 12, 9, 24, 23, 18, 1, 22, 11, 8, 14, 19, 3, 20, 17, 2, 21, 6, 4]. \n\n

*IP3 is generated after PLC hydrolyzes PIP2_45 {[5]-p.1,[16]-p.1,[7]-p.260,[12]-p.1,[9]-p(1)}\n<br>*IP3 is generated by PLC {[24]-p.2(282)}\n<br>*The PH domain of PLCg binds to IP3 with high affinity {[23]-p.7(481)}\n<br>*IP3 is a downstream pathway from PLCg {[18]-p.5,fig.3}\n<br>*IP3 is produced by PLC {[23]-p.1}\n<br>*PIP2_45 is hydrolyzed by phospholipses to generate IP3_145 and DAG {[15]-p(762, 765, 766)}\n<br>*The cleavage of PIP2_45 by PLC_generates DAG and IP3 {[10]-p(968, 976)}\n<br>*DAG and IP3 are generated by PLC from PIP2_45{[1]-p(1239),[22]-p(236)}\n<br>*PLCb produces IP3 and DAG {[4]-p(1638)}\n\n

*PIP2_45 is cleaved into IP3 and DAG by PLC_g when activated by EGFR {[11]-p.1,[13]-p.4,[8]-p(340)}\n<br>*The cleavage of PIP2_45 by PLC_generates DAG and IP3 {[10]-p(968)}\n<br>*PIP2_45 is a precursor for IP3 {[24]-p.2(282),[14]-p(502),[19]-p(1)}\n<br>*hydrolysis of PIP2 produces IP3{[3]-p.3,fig.2,[20]-p.1,[17]-p(232),[2]-p(6),[6]-p(1), [21]-p(3)} \n<br>*PIP2_45 is hydrolyzed by phospholipses to generate IP3_145 and DAG {[15]-p(762,765,766)}\n<br>*DAG and IP3 are generated by PLC from PIP2_45 {[1]-p(1239),[22]-p(236)}\n

S_155 1 S_118 1 S_175 1 S_118 1

RalGDS is a positive regulator [1, 6, 2, 11, 12, 10, 9]. CaM is a positive regulator [13, 1, 8]. AND34 is a positive regulator of Ral [7]. These are all in an OR [1, 8, 7]. \n\n

*RalGDS activates Ral {[1]-p(162), Fig. 4, [6]-p(10), [2]-p(2), [11]-p(3), Fig. 2, [12]-p(8), [10]-p(2), [9]-p(649), Fig. 9}\n\n<br>*RalGEF is a downstream target of Ras, specifically interacts with, and is activated by GTP-Ras. {[5]-p(1)}\n\n

*AND34 is an activator of Ral {[7]-all}\n

S_224 1 S_243 1 S_3 1

EGFR_Y1173 (Tyr_1173 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF/Epithelial|EGFR_EGFR_EGF]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa/Epithelial|EGFR_EGFR_TGFa]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer). This site can also be activated (phosphorylated) by Src when Integrins AND Cas AND EGFR_Free.\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [, 1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

S_195 1 S_157 1 S_99 1 S_52 1 S_214 1 S_194 1

Both Rab5 AND PIP3_345 are necessary for the recruitment of EEA1.{[2]-p(111)}\n\n

*The membrane recruitment of EEA1 depends on PI(3)P.{[4]-p(3745)}{[3]-p(698)} \n<br>*The concomitant presence of Rab5 and PIP3 allows the recruitment of Rab5 effectors EEA1 and Rabenosyn_5.{[2]-p(111)}\n

*Rab5 induces translocation of EEA1 from the cytoplasm to the membrane of early endosomes.{[5]-p(351)} \n<br>*EEA1 is a Rab5 effector that is essential for endosome fusion.{[3]-p(698)}{[2]-p(110)}{[1]-p(3)}\n<br>*Downstream effectors of Rab5 include EEA1 and syntaxin.{[6]-p(547)}\n<br>*The concomitant presence of Rab5 and PIP3 allows the recruitment of Rab5 effectors EEA1 and Rabenosyn_5.{[2]-p(111)}\n\n

S_192 1 S_74 1

*tion Mechanism==\n<br>*[[Src]] AND [[E-cadherin]] AND Ca-OFF activate Hakai [1].\n\n

S_244 1 S_229 1 S_126 1

ErbB2_Free represents monomeric ErbB2. The Off state of this node corresponds to non-existing ErbB2 on cell surface. On the other hand, the On state depicts the presence of a monomeric ErbB2, ready to dimerize to any of the other ErbBs. To simulate the model under different levels of ErbB2 expression, this node has an external node - ErbB2_Controller - which is responsible for providing the model with monomeric ErbB2s (ErbB2_Controller hence activates EGFR_Free).<BR>\nWhen dimerized, ErbB2 is removed from the pool of free, monomeric ErbB2's, therefore the following nodes representing active ErbB2 dimers act as negative regulators of ErbB2_Free: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR_EGFR homodimer on plasma membrane, activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR_EGFR homodimer on plasma membrane, activated by TGFa), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]], and [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]]. ([7, 2, 6, 8, 5, 1])\n\n

ErbB2_ErbB3 dimerization results in removing (i.e., turns off) a ErbB2 from the EGFR_Free pool.\n

EGFR_ErbB2 dimerization results in removing (i.e., turns off) a ErbB2 from the ErbB2_Free pool.\n\n

S_117 1 S_91 1 S_247 1 S_195 1 S_220 1 S_119 1 S_247 1

PIP_4 [44, 26, 50, 40, 46, 41, 32, 45, 23] AND PI5K [35, 6, 54, 7, 25, 9, 16, 3, 46, 41, 45, 23] can create PIP2_45.\nAnother way is if PTEN and PIP3_345 are ON, PTEN will dephosphorylate PIP3_345 and create PIP2_45 [27, 47, 50, 53, 19, 7, 50, 4, 55, 45].\nPLC_g OR PLC_B is a negative regulator [11, 44, 34, 49, 36, 16, 40, 7, 31, 28, 10, 2, 26, 54, 53, 1, 48] if PIP2_45 is ON [45] but are not strong enough to eliminate all the PIP2_45. \nPI3K phosphorylates PIP2_45 to PIP3_345 (thus eliminating PIP2_45), so it is also a negative regulator [28, 17, 10, 37, 18, 12, 43, 13, 55, 38, 20, 42, 5, 26, 24, 53, 54, 8, 52, 51, 45]. PI3K is also made not strong enough to use up all the PIP2_45.\nIf PIP2_45 is ON and there is no other regulation, it stays ON. \n\n

*PIP2_45 is downstream of PLC,PLD,PI3K {[28]-p(2), Fig. 2}\n<br>*PI3K's p110 subunint phosphorylates PIP2_45 yielding \nPIP3_345 {[17]-p(4)}\n<br>*PI3K converts PIP2_45 to PIP3_345 {[10]-p(1), [37]-p(64-Fig. 5)}\n<br>*PI3K phosphorylates PIP2_45 to produce PIP3_345 {[18]-p(3), Fig. 1, [12]-p(2), [43]-p(2), [13]-p(1), [55]-p(1), Fig. 1}\n<br>*The p110 subunit of PI3K phosphorylates PIP2_45 at position 3 {[38]-p(2, 3)}\n<br>*PI3K phosphorylates PIP2_45 on the D3 position to produce PIP3_345 {[20]-p(1), [42]-p(1), [5]-p(6), [45]-p(88, 89)}\n<br>*In vitro PI3K phosphorylates PIP2_45 {[26]-p(486)}\n<br>*PI3K phosphorylates PIP4 and PIP2_45 producing PIP2_34 and PIP3_345 {[24]-p(1)}\n<br>*In vivo, the preferred substrate of PI3Ks is PIP2_45 {[53]-p(1)}\n<br>*PIP2_45 is a substrate for PLC and PI3K {[54]-p(1)}\n<br>*Class I PI3K can phosphorylate PI4P and PIP2_45 {[8]-p(1)}\n<br>*The main activity of PI3K involves conversion of PIP2_45 into PIP3_345. {[52]-p(5), [51]-p(1)}\n<br>*Class I PI3K phosphorylates PI(4,5)P2 and generates PIP3 directly. {[15]-p(1)}\n\n

*PIP2_45 is downstream of PIP3_345 {[27]-p(2), Fig. 2}\n<br>*PTEN breaks PIP3_345 down to PIP2_45 {[47]-p(1170), Fig. 1, [50]-p(763, 765), Fig. 1}\n<br>*PTEN (3'-phosphatase) converts PIP2_34 to PIP_4 and PIP3_345 to PIP2_45 {[53]-p(1), [19]-p(3)}\n<br>*PIP3_345 produces DAG and IP3 from PIP2_45 {[7]-p(1)}\n<br>*PTEN specifically removes the 3OH phosphate of PIP3_345 into PIP2_45 {[50]-p(765), Fig. 1}\n<br>*PIP2_45 is generated by PTEN from PIP2_345 {[4]-p(215), Fig. 2}\n<br>*PTEN converts PIP3_345 back into PIP2_45 {[55]-p(2), Fig. 1, [45]-p(88)}\n\n

*PI5K catalyzes the synthesis of PIP2_45 {[35]-p.3(3585)}\n<br>*PI5K is responsible for synthesis of PIP2 {[6]-p(2), [54]-p(4)}\n<br>*PI5K produces pip2_45 {[7]-p(4), [25]-Fig. 1, [9]-(p(96), Fig. 1), [45]-p.402}\n<br>*PLD stimulates further synthesis of PIP2_45 via PA stimulation of PI5K {[16]-p(245), [45]-p.400}\n<br>*Rho directly effects PI5K, which in turn produces, PIP2_45. {[3]-p(2)}\n<br>*PIP_4 can be phosphorylated by PI5K to generated PIP2_45 {[46]-p(16919), [45]-p(88)}\n<br>*PIP5K type I phosphorates PIP_4 at D-5 position of the inositol ring, commits the final step in PIP2_45 synthesis in vivo {[41]-p(7840)}\n<br>*PI5K phosphorylates PtdIns-4-P at the position 5 to synthesize PIP2_45 OR PI4K phosphorylates PtdIns-5-P at the position 4 to synthesize PIP2_45 {[26]-p(501), [40]-p(3), [23]-p(78)}\n\n

S_118 1 S_219 1 S_118 1 S_196 1 S_74 1 S_208 1 S_106 1

NIK [15, 9, 20, 17, 11, 16, 19], Rho [1], Rac [9, 1, 13, 10, 19], Cdc42 [9, 1, 13], Ras [9, 19, 8], Gck [17, 9, 19, 7], Trafs [9, 7, 2, 14, 19]), and Grb2 AND Shc [9, 3] can all activate Mekk1. They are all in an OR. Other interactions are either not clear in their effects (e.g., Fak [18]) or are accounted for elsewhere (e.g., RhoGEF [5]) and are not included as inputs.\n\n

*Grb2 can bind Mekk1, and activated EGFR recruits the complex to Shc, lending more evidence that localization to the membrane is important for Mekk1 signaling. {[9]-p(844)}\n\n\n

*Trafs can activate Mekk1 directly. {[9]-p(836), [7]-all} \n<br>*Traf can interact with and activate Mekk1 {[2]-p(3)}\n<br>*TRAF2 binds MEKK1 and ASK1 {[14]-p(5)}\n<br>*TRAF6 binds MEKK1 and TAk1 via Tab2 {[14]-p(5)}\n<br>*Traf2 shown to interact (probably activate) Mekk1 {[19]-p(659)}\n

*Rho shown to interact (probably activate) Mekk1 {[19]-p(659)}\n<br>*Rho and Cdc42 each increase kinase activity of Mekk1 in vitro. {[1]-p(1876)}\n\n

*Mekk1 activated by GCK {[17]-p(38, 31-Fig. 2), [9]-p(836)}\n<br>*GCK shown to interact (probably activate) Mekk1 {[19]-p(659)}\n<br>*Gck can activate Mekk1 independently in vitro. {[7]-all}\n\n

*NIK binds to Mekk1 to activate SAPK {[15]-p(4), [9]-p(836), [20]-all}\n<br>*NIK binds Mekk1 {[17]-p(37)}\n<br>*N-terminus of MEKK1 associates with NIK and JNK {[11]-p(5)}\n<br>*NIK and HPK-1 phopshorylate Mekk1, but this wasn't shown to activate Mekk1 {[16]-p(3)}\n<br>*NIK shown to interact (probably activate) Mekk1 {[19]-p(659)}\n<br>*kinase-inactive Mekk1 can inhibit NIK activation of the SAPK pathway, suggesting that MEKK1 is a phyiological target of NIK {[17]-p(37)}\n\n\n

*Ras can directly bind (and activate) MEKK1 {[9]-p(828)}\n<br>*Ras shown to interact (probably activate) Mekk1 {[19]-p(659)}\n<br>*Small GTPases of the Ras superfamily (Ras, Rac, Cdc42) do not increase activity of Mekk1 when over expressed, but appear to be necessary for signaling. May be involved in localization. {[9]-p(844)}\n\n\n

*Mekk1 has been shown to bind to Cdc42 and Rac1 and kinase-dead Mekk1 can block Cdc42/Rac activation of JNK {[13]-p(11), [9]-p(844)}\n<br>*Small GTPases of the Ras superfamily (Ras, Rac, Cdc42) do not increase activity of Mekk1 when over expressed, but appear to be necessary for signaling. May be involved in localization. {[9]-p(844)}\n<br>*Rho and Cdc42 each increase kinase activity of Mekk1 in vitro. {[1]-p(1876)}\n\n

S_160 1 S_132 1 S_143 1 S_19 1 S_73 1 S_123 1 S_193 1 S_19 1 S_73 1 S_44 1 S_228 1 S_73 1 S_19 1

Alix is recruited by ESCRT_III or ESCRT_I.{[2, 4]}\n\n

*ESCRT_III is required for the recruitment of Alix.{[4]-p(645)} {[2]-p(157)} \n

*Alix binds to ESCRT_I/III complex.{[]}<br>*activated by X [2]<br>

S_102 1 S_15 1

Trafs are stimulated by IL1_TNFR [2, 1, 6, 3, 4, 5]\n\n

*IL1 stimulates Traf6 {[2]-p(1)}\n<br>*Occupancy of TNFR results in recruitment of Trafs {[1]-p(2, 4)}\n<br>*TNFR activate Trafs. {[6]-p(836)}\n<br>*Traf4 is a component of TNF signalling {[3]-p(2)}\n<br>*TNFR activation leads to recruitment of TRAF2 {[4]-p(5)}\n<br>*IL-1R recruits TRAF6 {[4]-p(5)}\n<br>*TNFR activates Trafs (through TRADD). {[5]-p(23756)}\n\n

S_61 1

Rab7 is activated by Rab5.{[2, 1]}\n\n

*Initially Rab5 activates Rab7 until Rab7 reaches a threshold upon which it inactivates Rab5 through a negative feedback loop.{[2]-p(354)}{[1]-p(4)} \n

S_192 1

ErbB4_Free represents ligand-free, inactive ErbB4. The Off state of this node corresponds to non-existing ErbB4 on cell surface. On the other hand, the On state depicts the presence of a ligand-free ErbB4, ready to be activated by any of its ligands. To simulate the model under different levels of ErbB4 expression, this node has an external node - ErbB4_Controller - which is responsible for providing the model with inactive ErbB4's (and hence activates ErbB4_Free).<BR>\nUpon binding to their ligand, ErbB4 dimerizes with other ErbB4's or other types of ErbB's. When dimerized, ErbB4 is removed from the pool of free, inactive ErbB4's, therefore the following nodes representing active ErbB4 dimers act as negative regulators of ErbB4_Free when ErbB4_Free was already ON: [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]], [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]],[[ErbB4_ErbB4/Epithelial|ErbB4_ErbB4]], and [[ErbB2_ErbB4/Epithelial|ErbB2_ErbB4]]. ([6, 2, 5, 9, 4, 1])\n\n

EGFR_ErbB4 dimerization results in removing (i.e., turns off) a ErbB4 from the ErbB4_Free pool.\n\n

ErbB2_ErbB4 dimerization results in removing (i.e., turns off) a ErbB4 from the ErbB4_Free pool.\n\n

ErbB4_ErbB4 dimerization results in removing (i.e., turns off) a ErbB4 from the ErbB4_Free pool.\n

S_125 1 S_34 1 S_214 1 S_220 1 S_20 1 S_202 1

External E-cadherin AND B-catenin are required for E-cadherin activation [4, 3, 2]. Hakai is a dominant negative to that positive regulation unless p120_catenin is ON[4, 3, 6]. IQGAP1 is also a dominant negative unless Rac or Cdc42 are ON [4, 3, 6, 1].\n\n

*p120-ctn promotes cell-cell adhesion by inhibiting E-cadherins from internalization [5]\n<br>*once E-cadherin translocates to the plasma membrane with the help of [[#Beta-catenin]], p120-ctn binds to E-cadherins via the JMD and prevents it from degredation. {[3]-p.9,10,[4]-p.662}\n<br>*internalization (specially via the clathrin-dependent pathway) of E-cadherin most likely requires p120_catenine dissociation. {[3]-p.9}\n<br>*p120 is essential for cadherin-based adhesion {[3]-p.10,[4]-p.662}\n<br>*Studies in Drosophila showed that p120_catenin null cells were viable. Indication of a positive effect of p120 on cadherin-related cell adhesion. {[3]-p.10}\n<br>*Studies in C. Elegans suggest that p120 is not essintial, but is a positive regulator of cadherins.{[3]-p.10}\n<br>*When p120 catenin binds to a cadherin, it loses the ability to bind to RhoA {[3]-p.13}\n\n

*IQGAP1 binds to E-cadherin and beta-catenin and weakening the cell-cell attachement {[1]-p.572}.\n<br>*Rac1 and Cdc42 inhibit the interaction of IQGAP1 between E-cadherin and beta-catenin {[1]-p.572}.\n

*Binds to phosphorylated motif in the JMD and induces the ubiquitination of E-cadherin. p120 is suggested to block the phosphorylation site by binding to JMD, therefore blocking possible internalization. Due to the fact that this tyrosine motif is absent in VE- and N-cadherin, Hakai only regulates E-cadherin. {[3]-p.13}\n<br>*Hakai targets E-cadherin for degredation in Src-dependent manner {[4]-p.662}\n<br>*Src pathway promotes Hakai binding to a tyrosine phosphorylated JMD of E-cadherin, targeting it for internalization {[7]-p.53}\n<br>*Upon Src phosphorylation of E-cadherin, Hakai binds E-cadherin to ubiquinate it {[6]-p.5127}\n\n

S_235 1 S_96 1 S_33 1 S_160 1 S_132 1 S_116 1 S_90 1

EGFR_Y1086 (Tyr_1086 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer). This site can also be activated (phosphorylated) by Src AND Integrins AND Cas AND EGFR_Free.\n\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [2, 1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

S_214 1 S_195 1 S_52 1 S_194 1 S_157 1 S_99 1

PIP2_34 [6, 24, 11, 12, 31, 27, 2] OR PIP3_345 [27, 2, 4, 30, 25, 9, 11, 7, 3, 16, 12, 17, 14, 31, 22, 23, 21] are required only to localize PDK1. However, PDK1 has (different) activity in the cytosol and the membrane, so PI3P-mediate localization does not determine the ON/OFF status of PDK1. This means that, from a logical perspective, PI3P's are not inputs to PDK1. Thus, in order to discriminate 'ON in the cytosol' from 'ON in the membrane,' PDK1 and PI3P's will appear as inputs to the appropriate nodes and PI3P's will not appear as inputs to PDK1.\nAs far as the logical inputs to PDK1, it has been reported that the PDK1 kinase activity is constitutively active [9, 5, 19, 28], but more recent reports [1, 20] have provided evidence that PDK1 activity is regulated, perhaps by a Src kinase family member or p90RSK. Since a constitutively active version of PDK1 would drop out of the network (as far as logic), we will make PDK1 kinase activity dependent on either Src OR p90RSK.\n\n

S_131 1 S_244 1

Cas is activated by Src AND Fak [19, 8, 30, 24, 12, 6, 18, 13, 33, 16, 36, 23, 2, 32, 20, 14, 25, 37, 34, 10, 5, 7, 31, 15, 21, 3, 22, 11, 26, 9, 4]. PTPPEST deactivates Cas [30, 18, 13, 35, 1, 38, 33, 24, 29] after Cas has been activated.\nThere is literature that says that PTP1b is also a negative regulator of Cas [30, 6, 27, 16, 28, 5], but there is a newer paper that shows it is not [17]. Therefore, PTP1b will be left out.\n\n

*Cas is activated by Src {[19]-p(7), [8]-p.18(138), [30]-p(1), [24]-p(7937)}\n<br>*Src can phosphorylate Cas {[12]-p(529), [6]-p(2), [18]-p(3)}\n<br>*Activated Src phosphorylates Cas. {[13]-p(3)}\n<br>*Src has been shown to directly promote tyrosine phosphorylation of Cas. {[33]-p(4)}\n<br>*Src assocaition with FAK can potentiate the phosphoralation of Cas {[16]-p(458)}\n<br>*Cas is a potential substrate of Src {[36]-p(9), [23]-p(31), [2]-p(234)}\n<br>*p130Cas is tightly bound to v-Src. {[32]-p(1)}\n<br>*Cas is bound by Src and FAK family kinases {[20]-p(6352), [14]-p(7)}\n<br>*Cas is a target of hyperphosphorylation by Src. {[25]-p(117)}\n<br>*Src phosphorylates focal adhesion components, such as talin, paxillin, Cas, and Fak itself on Tyr925, leading to signalling functions {[37]-p(1)}\n<br>*p130cas is a substrate of Src {[34]-p(123), [10]-p(7947), [5]-p(279)}\n<br>*The dual FAK-Src PTK complex promotes the tyrosine phosphorylation of SHC, Pax, and p130Cas {[7]-p(2), [31]-p(2690)}\n\n

*PTP-PEST and PTP-1b target Cas and may specifically inhibit some of the signals downstream of FAK {[30]-p(2)}\n<br>*Overexpression of PTP-PEST results in significently reduced levels of tyrine phosphorylated Cas {[18]-p(4), [13]-p(3)}\n<br>*Cas is dephosphorylated by PTP-PEST {[35]-p(1), [1]-p(166), [38]-p(24422)}\n<br>*Cas is inhibited by PTP-PEST {[35]-p(1, Fig.1)}\n<br>*Cells expressing activated PTP-PEST exhibited a decrease in levels of tyrosine-phosphorylated Cas. {[33]-p(4)}\n<br>*Dephosphorylation of Cas via PTP-PEST is necessary for modulation of Crk binding. {[33]-p(5)} \n<br>*PTP-PEST can bind p130CAS and paxillin and induce their dephosphorylation in vivo {[24]-p(7940)}\n<br>*PTP-PEST binds to p130Cas. {[13]-p(3)}\n<br>*PTPPEST can dephosphorylate several signalling proteins that participate in TCP signalling, such as Shc, Pyk, Fak and Cas {[29]-p(21)}\n

*FAK provides binding sites for CAS and Graf {[15]-p(2)}\n<br>*Cas is phosphorylated by FAK {[15]-p(12), [18], [33]-p(3),[31]-p(2689)}\n<br>*Cas directly interacts with FAK {[21]-p(11), [6]-p(2)}\n<br>*Cas binds to FAK through its SH3 domain {[3]-p(1), [16]-p(441, 442), [22]-p(1), [11]-p(59), [13]-p(2), [26]-p(1411)} \n<br>*FAK initiate Cas phosphorlation {[16]-p(443)}\n<br>*Cas is a potential substrate of Fak {[2]-p(234)}\n<br>*Cas and Fak colocalize in focal adhesions; Cas can be a substrate of Fak {[18]-p(4)}\n<br>*Pax is bound by Src and FAK family kinases {[20]-p(6352)}\n<br>*Both p130cas and paxillin associate with FAK and both are phosphorated by FAK, both have been linked to Rac activation. {[9]-p(574), Fig.1} \n<br>*p130Cas is heavily phosphorylated upon integrin stimulation and, in part, this phosphorylation is attributed to FAK {[13]-p(2)}\n<br>*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[4]-p.2(3584)}\n<br>*Cas binds to FAK and are tyrosine phosphorylated either directly by FAK or through cooperative interaction between Src and FAK. Following tyrosine phosphorylation, the Cas acts as a docking molecule, assembling additional SH2domain containing proteins, such as Crk. {[25]-p(114)}\n<br>*Cas can interact with Fak. {[33]-p(3)}\n\n

S_244 1 S_135 1 S_75 1 S_129 1

S_130 1 S_108 1 S_43 1 S_130 1 S_212 1

Erk [7, 17, 2, 12, 14, 18, 13, 10, 11, 9, 6, 16] AND PDK1 [11, 13, 4, 5, 15, 19, 3, 8, 16] are required for the activation of p90RSK when p90RSK is inactive [3].\n\n

*PDK1 also activates RSK. Note that both Erk and PDK1 have to activate RSK to achieve its full activation {[11]-p(5)}\n<br>*p90RSK needs PDK1 phosphorylation to be catalically active {[13]-p(6)}\n<br>*PDK1 also phosphorylates p90Rsk {[4]-p(2), [5]-p(7), Fig. 1}\n<br>*PDK1 phosphorylates p70S6K and PAK in PI3K-dependent manner; and PKA,PKC, p90Rsk PI3K-independent manner {[15]-p(5)}\n<br>*PDK1 phosphorylates p90RSK in vitro. {[19]-p(7)}\n<br>*P90RSK, p70S6K and Akt are activated with different temporal regulations while some substrates are phosphorylated by PDK1 constitutively {[3]-p(1)}\n<br>*HM phosphorylation of PDK1 is crucial for the interaction of PDK1 with RSK and S6K {[3]-p(2)}\n<br>*PDK1 regulates and is required for activation of Rsk. {[]-p(2), [8]-p(162)}\n\n

*p90RSK is downstream of ERK {[17]-p(4), Fig. 1, [2]-p(5), [14]-p(2-Fig. 1)}\n<br>*p90RSK is activated by Erk {[18]-p(3), Fig. 1, [13]-p(2), [10]-p(3)}\n<br>*Erk activates C terminal of RSK which leads to activation of the N terminal {[11]-p(3, 5)}\n<br>*Erk phosphorylates Rsk {[7]-p(6), [9]-p(1), [12]-p(85)}\n<br>*p90RSK is an ERK2 docking site. {[6]-p(196)}\n\n\n

S_234 1 S_131 1 S_128 1

RhoGDI is a dominant negative regulator of Cdc42 [32, 35, 33, 1, 7]. This is true whether Cdc42 is ON or OFF [9]. Src enhances RhoGDI's negative influence [17] and therefore will be required for RhoGDI to have any effect.\nRalBP1 [21, 15, 26, 22], p190RhoGap [30, 25], and Graf [3] are GAP's and therfore negative regulators. When Cdc42 is ON, they turn it OFF, unless Pix_Cool is ON to keep Cdc42 ON [24]. \nPix_Cool is a GEF and therefore a positive regulator [27, 7, 24]. In order to regulate Cdc42, Pak and Gbg_i must be ON [24] and Rac AND Cdc42 must be OFF because when they are ON, they block the activating domain of Pix_Cool [24, 12]. IQGAP1 keeps Cdc42 ON when already ON in absence of negative regulators. [4, 11, 19]\n\n

*Graf is a GAP for Cdc42 and Rac {[3]-p(9576)}\n\n

*IQGAP1 binds to Cdc42 {[4]-p(5)} \n<br>*IQGAP1 inhibits the intrinsic GTPase activity of Cdc42 {[19]-p.572}, which seems to be strong enough to increase the pool of active Cdc42 in a cell {[11]-p.8}.\n<br>*IQGAP functions as a scaffold, also responsible for the translocation of Cdc42 to plasma membrane, which is required for its activity {[11]-p.8}.\n\n

*p190RhoGAP can catalyze hydrolysis of Rho A,B, and C equally well but works with weakly on Rac or Cdc42 {[30]-p(2)}\n<br>*p190RhoGAP shows catalytic GAP activity towards Rac1. {[25]-p(6)}\n\n

*RalBP1 is a GTPase-activating protein for Rac1 and Cdc42 {[21]-p(162, Fig.4), [15]-p(8), [22]-p(1113)}\n<br>*RalBP1 can potentially regulate Rac and Cdc42 {[26]-p(4)}\n\n

*Src phosphorylates Tyr64 on Cdc42 {[17]-p(3)}\n\n

*RhoGDI binds to Cdc42 to maintain its GDP state until it's removed from cytosol.The mechanism unknown {[32]-p(165, 167), [35]-p(1), [33]-p(5)}. ->Might have a significant effect on our logic. ->Also,the connection should be NEGATIVE.\n<br>*RhoGDI has the property of inhibiting both intrinsic- and GAP-stimulated GTP hydrolysis by Rac andCDC42Hs. {[1]-p(26206)}\n<br>*RhoGDI binds to activated forms of Cdc42, and mediates their release from membranes. {[7]-p(4)} \n<br>*Despite being a negative regulator of Cdc42 activation and GTP hydrolysis, RhoGDI plays an essential role in Cdc42-mediated cellular transformation. {[9]-p(1)}\n<br>*The first step of a two step interaction process between Cdc42 and RhoGDI is the rapid binding between Cdc42 and RhoGDI {[9]-p(1)}\n<br>*RhoGDI can bind with equal affinity to GDP and GTP bound forms of Cdc42, and is capable of inhibiting the GTP hydrolytic activity of Cdc42. {[9]-p(1)} \n<br>*Interaction of activated Cdc42 wtih RhoGDI is essential for Cdc42-mediated cellular transformation. {[9]-p(1)} \n<br>*RhoGDI binds well to Cdc42. {[31]-p(1)}\n\n

S_40 1 S_222 1 S_21 1 S_160 1 S_132 1 S_205 1 S_244 1 S_132 1 S_33 1 S_71 1 S_199 1 S_88 1 S_205 1 S_244 1

cAMP is absolutely required to be ON for PKA to be ON [10, 6, 15, 8, 18, 22, 17, 5] and will keep it ON, unless PP2A is present. PP2A is a negative regulator, and deactivates PKA if PKA is ON [19]. PDK1 is necessary for the assembly of the mature enzyme [20, 16, 9, 21, 12], but not sufficient for activity [15]. PDK1 only has an effect on inactive PKA [12, 14].\n\n

*PP2A dephosphorylates PKA at Thr_197, which is required for activity of PKA {[19]-p(1)}\n

S_128 1 S_188 1 S_43 1 S_133 1 S_133 1 S_188 1 S_43 1 S_133 1

ErbB3_Y1243 (Tyr_1243 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1243 (Tyr_1243 site of ErbB3) is activated upon receptor dimerization [].\n\n

S_20 1 S_99 1 S_91 1

For the model, Fak is defined as ON when it is autophosphorylated and associated with integrins [45, 41, 8, 11, 48, 54, 6, 23, 13, 35, 9, 3, 50, 26, 7, 20, 24, 53, 16, 43, 40, 30, 29, 1, 25, 15, 20].\nSince Talin is the protein that recruits and binds Fak to Integrins [42, 14, 20], Talin AND Integrins must be ON for Fak to be ON. (Note that Integrins ON implies the presence of ECM [see Integrins], so ECM is indirectly required for Fak to be ON.\nWhen Fak is ON, it attracts Src which phosphorylates Fak on additional sites, allowing downstream signaling [19, 41, 14, 22, 39, 24, 14, 37, 45, 54, 12, 20, 36, 57, 38, 43, 17, 21, 29, 10, 1, 32, 59, 18, 53, 25, 26, 47] and will keep FAK ON.\nPTEN is a negative regulator of Fak because it dephosphorylates the autophosphorylation site of Fak [37, 45, 54, 6, 20, 7, 27, 51, 34, 60, 43, 5, 44, 49, 55]. It will be dominant when Fak is ON.\nSumming up the logic, if Fak is ON and PTEN is ON, Fak will turn OFF. If Fak and Src are ON, Fak will stay ON. If Fak is OFF, PTEN and Src have no effect on Fak, so Talin AND Integrins ON means Fak will turn ON.\n\n

*Src phosphorylates Fak {[19]-p(17170, 17175),[41]-p(3),[14]-p(3)}\n<br>*Active Src phosphorylates Fak. {[14]-p(3)}\n<br>*Src phosphorylates FAK on y295 {[22]-p.6,[47]-p(321)}\n<br>*Src phosphorylates 4 tyrosine sites on Fak {[39]-p.18(138),[24]-p.30}\n<br>*When src phosphorylates Y576 and 577, Fak is activated. When src phosphorylates Y925, it provides binding spot for Grb2. {[24]-p.30,[14]-p(2),[47]-p(321)} :this links FAK to activation of Ras and the MAPK pathway. {[14]-p(2)} \n<br>*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[37]-p.2(3584)}\n<br>*An important event in activation of FAK is phosphorylation of the tyrosine residues in the activation loops. These residues are phosphorylated by Src family kinases {[45]-p.7}\n<br>*Initially activated Src can phosphorylate FAK on the activation residues, activating FAK {[45]-p.9}\n<br>*Src phosphorylates Fak at Tyr925, creating a binding site for the complex of the adapter Grb2 and Ras guanosine 5-triphosphate exchange factor mSOS {[54]-p.1-2}\n<br>*v-Src can phosphorylate Fak {[12]-p.529} \n<br>*Src phosphorylated Fak and activates FAK {[20]-p(441, 443, 444, 457)} \n<br>*Fak is activated by Src {[36]-p(8)}\n<br>*Fak is potential substrate of Src {[57]-p(9)}\n<br>*Src phosphorylates and activates FAK {[38]-p(8)}\n<br>*Association between FAK and Src leads to phosphorylation of FAK. {[43]-p(1)}\n<br>*Fak is a substrate of v-Src {[17]-p(2)}\n<br>*Cas-protein-associated kinase FAK undergoes autophosphorylation, creating a binding site for Src-family kinases. {[21]-p(114)}\n<br>*FAK is a Src substrate {[29]-p(127),[10]-p(7947)} \n<br>*FAK becomes autophosphorylated at Tyr397 either directly by integrin clustering or after phosphorylation of tyrosines 576 and 577 by Src {[1]-p(2327),[32]-p(223)}\nSrc can both bind to p125FAK and phosphorylate it {[59]-p(7974)}\n<br>*v-Src binds to FAK and induces its phosphorylation {[18]-p(4)}\n<br>*Srk activity in complex with FAK promotes phosphorylation of Fak, becoming a binding site for Grb2. { [53]-p(2)}\n<br>*Src mediated binding to Fak leads to the generation of an activated Src-Fak signaling complex. {[53]-p(2)}\n<br>*Src facilitates maximal Fak activation through phosphorylation at tyr_576 and tyr_577 within the Fak kinase domain; Src phosphorylates additional sites at tyr861 and tyr_925, the latter serving as a Grb2 binding site. {[53]-p(2)}\n<br>*The binding of Src with FAK at tyrosine 397 leads to phosphorylation of the remaining sites of tyrosine phosphorylation in FAK, namely Y407, 576, 577, 861 and 925 {[25]-p(7936),[26]-p.1410-11}\n\n

*Talin binds and recruits Fak to integrins (causing Fak to autophosphorylate).{[14]-p(107,108), [42]-p(57),[20]-p(442,452)}.\n\n

*The co-localization of FAK with integrins in focal adhesion is a prerequisite for cell adhesion-dependent activation of FAK signaling {[45]-p.6}\n<br>*Integrin engagement leads to tyrosine phosphorylation of FAK {[48]-p.2,[8]-p(1),[41]-p(3),[20]-p(152)}\n<br>*Fak-Src complex is regulated by integrins {[11]-p.2}\n<br>*Integrins activate FAK {[54]-p.1, [6]-p.13,[23]-p.10,[13]-p(1),[35]-p(1),[9]-p.1534}\n<br>*Fak binds to integrins directly {[23]-p.10,[3]-p.2,[2]-p(212),[50]-p(1),[26]-p.1409}\n<br>*Fak shows both increased kinase activity and tyrosine phosphorylation in response to integrin activation {[7]-p.1}\n<br>*Fak can be activated by integrin {[20]-p(436, 451, 453, 460)} \n<br>*Integrin activation stimulates autophos. (and activation) of Fak (Y397). {[24]-p.30,[26]-p.1410}\n<br>*Integrin clustering induces FAK coclustering, and enhances phosphorylation. {[8]-p(2)}\n<br>*Clustering of Integrins promotes Fak activation. {[53]-p(2)}\n<br>*FAK localizes to focal adhesions and becomes highly phosphorylized upon integrin clustering. {[16]-p(1),[50]-p(1)}\n<br>*Translocation to the membrane by integrins activates FAK {[50]-p(3)} \n<br>*Consequence of integrin clustering is the recruitment of FAK, followed by rapid autophosphorylation which facilitates the binding of Src and PI3K. {[43]-p(1)}\n<br>*In respones to integrin engagement, several tyrosine kinases are activated, including Fak and Src. {[40]-p(573)}\n<br>*Integrins interact with Fak and Src kinase family {[30]-p(1)}\n<br>*FAK respons to integrin engagement by autophosphorylation of its tyrosine-397 which , in turn, creates a binding site for the Src fmily kinases. {[29]-p(127)}\n<br>*FAK becomes autophosphorylated at Tyr397 either directly by integrin clustering or after phosphorylation of tyrosines 576 and 577 by Src {[1]-p(2327)}\n<br>*Integrins directly bind to Fak. {[53]-p(2)}\n<br>*Tyrosine phosphorylation of FAK and its catalytic activity are stimulated upon integrin-depend cell adhesion. It is unclear exactly how clustering of integrins leads to activation FAK {[25]-p(7930)}\n<br>*Integrin clustering and actin polymerization are required for FAK signaling {[15]-p(85)}\n\n

*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[37]-p.2(3584)}\n<br>*The most convincing evidence to date (2001) suggests that PTEN catalyzes dephosphorylation of FAK {[45]-p.9}\n<br>*PTEN dephosphorylates the autophosphorylation site of FAK {[45]-p(10,11)}\n<br>*PTEN dephosphorylates FAK and Shc {[54]-p.2,[51]-p(3),[34]-p(6)} which leads to inhibition of cell migration {[34]-p(6)}\n<br>*FAK is a substrate of PTEN {[6]-p.1}\n<br>*PTEN associates with FAK directly and can reduce its tyrosine phosphorylation as well as that of a potential downstream effector Cas {[6]-p.2}\n<br>*PTEN regulates FAK phosphorylation {[7]-p.2}\n<br>*PTEN directly bind to FAK and reduce its phosphorylation {[52]-p(1174),[60]-p(5)}\n<br>*PTEN is a negative regulator of FAK {[20]-p(467)}\n<br>*PTEN dephosphorylates FAK {[27]-p(973),[43]-p(1),[5]-p(278),[55]-p(2678)}\n<br>*PTEN inhibits cell migration and invasion through a process that involves dephosphorylation of Fak and Cas {[49]-p(4)}\n<br>*PTEN directly associates with FAK and can reduce its tyrosine phosphorylation as well as its potential downstream effector Cas {[44]-p(5)}\n

S_200 1 S_218 1 S_196 1 S_135 1 S_244 1 S_135 1 S_196 1 S_135 1

ErbB2_Y1139 (Tyr_1139 site of ErbB2) is activated when ErbB2 dimerizes with [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] [1].\n\n

ErbB2_Y1139 (Tyr_1139 site of ErbB2) is activated upon receptor dimerization [1].\n

ErbB2_Y1139 (Tyr_1139 site of ErbB2) is activated upon receptor dimerization [1].\n\n

S_195 1 S_91 1 S_220 1

In the model, Vinculin (Vinc) is considered ON when it is in the open conformation. Opening Vinc is a two step process [8]. Talin is required for one step [17, 9, 15, 16, 8, 12, 10]. It's not certain what is responsible for the second step; originally PIP2_45 was thought to be an activator of Vinc [9, 5, 15, 11, 17, 18, 10], so it might be a candidate. However, there is newer evidence that indicates that PIP2_45 is not required for activation, but, rather is involved in the negative regulation of Vinc [8, 21]. \nAt this time, Src is a reasonable candidate [12, 8] and will be used. Therefore Vinc is ON (in the open conformation) is Src AND Talin are ON.\nHowever, Src is not necessary for Vinc to be ON if Vinc was ON and Talin are both ON. Since Vinc is a bridge between Talin and Actin, they keep Vinc in the open configuration [16].\nActin binding to Vinc can be displaced by PIP2_45 [17, 7]. In this case, Vinc will turn OFF (unless Src is ON) because Vinc's autoinhibition is dominant to the activating effect of Talin [8].\n\n

*PIP2_45 makes vinculin unfold and expose the talin binding site, which is critical for FA localization. {[9]-p(379), [10]-p(445)}\n<br>*PIP2_45 controls its molecular association with focal adhesions {[2]-p(5)}\n<br>*PIP2_45 is known to conformationally activate vinculin {[5]-p(96, Fig. 1), [15]-p(135)}\n<br>*Vinculin's binding PIP2_45 expises cryotic binding sites for other proteins, including Talin. {[11]-p(577)}\n<br>*Vinculin is considered to be activated by PIP2_45 {[17]-p(833)}\n<br>*Vinculin tail can also bind PIP3 {[17]-p(833)}\n<br>*Some are skeptical that PIP2 is a relevant activator of vinculin because the interaction is very weak. At best it is a co-activator, but not known if it complements talin. {[8]-p.17115}\n<br>*Two-step activation of Vinculin: PIP2_45 opens up vinc, which then binds to talin {[1]-all}\n<br>*PIP2 may bind to vinculin and release autoinhibition. {[12]-p.4234}\n<br>*Binding of PIP's or talin can relieve autoinhibition of vinculin, making it competent to bind actin. {[12]-p.4245}\n<br>*PIPKIg is recruited to FA through binding to talin. This binding increases the activity of PIPKIg, resulting in production of more PIP2_45, which then regulates talin, vinc, and other FA proteins. {[3]-p(697),[23]-p(88)} \n<br>*Vinc requires PIP2_45 for activity {[6]-p(83)}\n<br>*Binding of PIP2 is thought to disrupt the head to tail association, because it unmasks the talin-binding site. Although it is needed to disrupt tail - head interaction, PIP2 activated vinculin does not bind to actin. {[18]-p(258)}\n

S_4 1 S_218 1 S_137 1 S_118 1 S_218 1 S_244 1

PIP3_345 [6, 44, 26] OR PIP2_45 [24, 3, 26, 10, 12, 31, 13, 6, 38, 44, 21, 37, 17, 18, 34] are required (but not sufficient) for PLD activity. Required co-factors include ARF [43, 11, 3, 9, 12, 38, 39, 37, 20, 14, 7, 1, 24, 26, 31, 27, 42, 41, 18, 22, 34, 4, 44, 21] OR Rac[26, 43, 38, 44, 34, 23] OR Rho [28, 24, 7, 3, 43, 38, 44, 30, 15, 22, 18, 35, 34, 23] OR Cdc42 [34, 23, 43, 44, 33] OR PKC [43, 9, 14, 3, 5, 24, 26, 38, 39, 7, 41, 18, 35, 34, 44] OR {Ral AND ARF} [36, 8, 28, 3, 42, 18, 34, 16, 29].\nActin (when monomeric [OFF]) is a negative regulator [45, 34, 44], but ARF is dominant to it [34]. \n\n\n

*Monomeric G-actin inhibits PLD activity through inhibiting the initiation steps of catalysis and polymerized F-actin auguments PLD activity by promoting the interaction of the enzyme with memberance {[45]-p(231, 239)}\n<br>*Purified b-actin potently inhibits PIP2_45_ and oleate_PLD2 activity; a-actinin inhibites PLD2 activity in an interaction-dependent and an Arf1-reversible manner {[34]-p(28252)}\n<br>*b-actin has been observed to inhibit both oleate- and PIP2_45-dependent PLD activityes by a mechanism that did not involve PIP2_45 sequstration or metabolism, but which could be partially relieved by ARF {[44]-p(237)}\n

*PLD binds directly and independently to ARF,Rac1 and PKC {[26]-p(8)}\n<br>*PLD was shown to be activated by RhoA,Rac1 and CDC42 {[43]-p.21(495), [38]-p(1), [44]-p(235), [25]-p.400}\n<br>*PLD1 has low basal activity in the presence of PIP2_45 and can be activated by PKCa, Rac1, ARF1, RalA, CDC42. {[34]-p(28252)}\n<br>*PLD has also been shown to be regulated by RhoA- and Rho-kinasem as well as by Rac1 and Cdc 42 {[23]-p(78480)}\n\n

*PLD upregulation is both Ral and Rho dependent. Ral and Rho can each interact directly with PLD {[28]-p(230)}\n<br>*PLD1 is markedly stimulated by PIP2_45, PKC, ARF, and Rho {[24]-p(1)}\n<br>*Rho families activates PLD {[3]-p(36, 39), [7]-p(1)}\n<br>*PLD was shown to be activated by RhoA,Rac1 and CDC42 {[43]-p.21(495), [38]-p(1), [44]-p(235)}\n<br>*Activation of PLD1 by Arf, Rho and PKC is synergestic by binding to specific regions of the PLD1 molecule {[38]-p(2)}\n<br>*Rho is thought to activate PLD. Rho regulates PLD activity cooperatively with Arf. {[30]-p(466)}\n<br>*PLD1 is regulated by different activating signals including receptor_ and nonreceptor_tyrosine kinases through ARF, RhoA, PKC, and RalA {[18]-p(234)}\n<br>*RhoA binds to PLD and activates PLD {[15]-p(1)} \n<br>*Arf and RhoA are the PLD activators, and PIP2_45 are crucial for this PLD activity {[22]-p(1234, 1236)}\n<br>*Rho and its upstream regulator G13 activate only PLD1 {[35]-p(140)}\n<br>*PLD1 has low basal activity in the presence of PIP2_45 and can be activated by PKCa, Rac1, ARF1, RalA, CDC42. {[34]-p(28252)}\n<br>*PLD has also been shown to be regulated by RhoA- and Rho-kinasem as well as by Rac1 and Cdc 42 {[23]-p(78480), [25]-p.400}\n\n

*PLD1 is markedly stimulated by PIP2_45, PKC, ARF, and Rho {[24]-p(1), [25]-p.400}\n<br>*PIP2_45 is a required cofactor for PLD activation {[3]-p(5)}, both PLD1 and PLD2 [25]-p.400, 401}.\n<br>*PIP2_45 stimulates the activity of PLD {[10]-p(1), [40]-p.889}.\n<br>*PIP2_45 is essentialy required for PLD through N-terminal PH domain {[26]-p(1)} - but it's not able to activate it by itself {[26]-p(9)}\n<br>*PIP2_45 enhances activation of PLD and Arf activation by Arf GEF {[12]-p(251)}\n<br>*ArF-1 acts in concert with PIP2_45 to activate PLD {[31]-p(768), Fig. 2}\n<br>*PIP2_45 positively regulates PLD and acts synergistically with activated Arf on PLD {[13]-p(3)}\n<br>*PIP2_45 and PIP3_345 activate PLD1 (?directly?-most likely through Arf) {[6]-p(2)}\n<br>*In vitro, PIP2_45 is a requirment for PLD1 activity. They interact directly {[38]-p(3)}\n<br>*In the presence of ARF1 and Rac1, both natural polyunsaturated PIP2_45 and synthetic dipalmitoyl PIP2_45 are effective activators of PLD1b {[44]-p(236)}\n<br>*PLD1 and PLD2 have almost an absolute requirement for PIP2 {[21]-p(94)}\n<br>*PLD is an additional effector of phosphoinsited - its activity and stimulation by ARF stringently require phosphoinositides (direct interaction) {[12]-p(251)}\n<br>*Phosphoinositides are required for Arf activation/disactivation and for PLD activation {[12]-p(251)}\n<br>*PIP2_45 is a required cofactor for PLD activation {[6]-p(3), [37]-p(1)}\n<br>*PIP2_45 is required for activation of PLD1, but is also dependent on ARF nad PKC {[17]-p(1)}\n<br>*Arf1 required PIP2_45 as a cofactor for PLD activation {[18]-p(234)}\n<br>*PLD2 also depends on PIP2_45 but has a higher basal activity than PLD1 {[34]-p(28252)}\n\n

*PIP2_45 and PIP3_345 activate PLD1 (?directly?) {[6]-p(2)}\n<br>*PIP3_345 has also been reported to stimulate PLD {[44]-p(237)}\n<br>*PLD activity is PI3K dependent {[26]-p(2)}\n<br>*PLD activity is not stimulated with GDP ligand.Therefore, Rac or ARF has to activate it first and that won't happen without PI3K {[26]-p(9)}\n<br>*PLD binds directly to PIP3 via its PX domain {[25]-p.400}.\n\n

*PLD is activated by PKC {[43]-p.21(495, 496), [5]-p(6), [3]-p(35, 36, 37, 40), [9]-p(1), [14]-p(33818)}\n<br>*PLD1 is markedly stimulated by PIP2_45, PKC, ARF, and Rho {[24]-p(9744)}\n<br>*PLD binds directly and independently to ARF,Rac1 and PKC {[26]-p(8)}\n<br>*Activation of PLD1 by Arf, Rho and PKC is synergistic by binding to specific regions of the PLD1 molecule {[38]-p(2)}\n<br>*PKC stimulates PLD activity {[39]-p(9), [7]-p(1)}\n<br>*PLD1 activity is regulated by PKC and members of the Rho, ARF and Ras/Ral families {[41]-p(1)}\n<br>*PKC-a can stimulate PLD activity and PKC-a occurs synergistically with ARF and RhoA {[18]-p(231)}\n<br>*PKC is a common activator of both PLD1 and PLD2 in vivo although PLD2 shows higher basal activity {[35]-p(140)}\n<br>*PLD1 has low basal activity in the presence of PIP2_45 and can be activated by PKCa, Rac1, ARF1, RalA, CDC42. {[34]-p(28252)}\n<br>*PKC has been reported to phosphorate PLD1 on serine-2, threonine-147 and serine-561 {[44]-p(236)}\n<br>*PKCa and PKCd have negative effects on PLC activity {[44]-p(235)}\n<br>*Phosphorylation of PLD (by PKC) MAY be required {[41]-p(7)}\n<br>*PKC-mediated activation of PLD can occur independently of kinase activity {[3]-p(4)}\n\n

*Arf activates PLD {[43]-p.20(494), [11]-p(1), [3]-p(36, 39), [9]-p(1), [12]-p(245), [38]-p(2), [39]-p(1), [37]-p(2), [20]-p(4), [14]-p(33818), Fig. 8, [7]-p(1), [25]-p.400}\n<br>*Activation of PLD is a major downstream effect of ARF6. {[1]-p(3)}\n<br>*Arf stimulates the activity of PLD {[24]-p(1), [38]-p(1)}\n<br>*PLD1 is markedly stimulated by PIP2_45, PKC, ARF, and Rho {[24]-p(1)}\n<br>*PLD binds directly and independently to ARF,Rac1 and PKC {[26]-p(8)}\n<br>*ArF-1 acts in concert with PIP2_45 to activate PLD {[31]-p(768), Fig. 2}\n<br>*Activation of PLD1 by Arf, Rho and PKC is synergestic by binding to specific regions of the PLD1 molecule {[38]-p(2)}\n<br>*PLD1 activity is regulated by PKC and members of the Rho, ARF and Ras/Ral families {[41]-p(1)}\n<br>*ArF stimulates PLD activation at the plasma membrane {[27]-p(79)}\n<br>*Both RalA and ARF6 together lead to the elevation of PLD activity {[42]-p(645), Fig. 9}\n<br>*Arf1 coimmunoprecipitates with PLD1 and that the ARF1-dependent PLD activation is induced by the ldirect interaction between ARF1 and PLD1 {[18]-p(231)}\n<br>*Arf and RhoA are the PLD activators, and PIP2_45 are crucial for this PLD activity {[22]-p(1234, 1236)}\n<br>*Both PLD1 and the truncated form of PLD2 are activated by in vitor by ARF1 more effectively than by ARF6 {[14]-p(33818)}\n<br>*Arf1 could steer the PLD2 activity in positive direction regardless of the inhibitory effect of b-actin on PLD2 {[34]-p(28252)}\n<br>*PLD1 has low basal activity in the presence of PIP2_45 and can be activated by PKCa, Rac1, ARF1, RalA, CDC42. {[34]-p(28252)}\n<br>*Arf-GTP binds to and activates PIPKs and PLD {[4]-p(398), table 2}\n<br>*Six mammalian ARFs are all reported to activate mammalian PLD1 activity with little if any differences in potency and efficacy {[44]-p(234)}\n<br>*PLD is known to be regulated by ARF and Rho. {[1]-p(7)}\n<br>*PLD is activated by ARF GTPases, and the activities of PLD and PIP5K can be amplified by reciprocal stimulation via their products PA and PIP2 {[21]-p(90-Fig. 2)}\n<br>*All Arfs are allosteric activators of PLD {[2]}\n\n

*PLD1 has low basal activity in the presence of PIP2_45 and can be activated by PKCa, Rac1, ARF1, RalA, CDC42. {[34]-p(28252)}\n<br>*PLD has also been shown to be regulated by RhoA- and Rho-kinasem as well as by Rac1 and Cdc 42 {[23]-p(78480)}\n<br>*PLD was shown to be activated by RhoA,Rac1 and CDC42 {[43]-p.21(495), [44]-p(235)}\n<br>*Cdc42 and Rac modulate PLD1. {[33]-p(1), [25]-p.400}\n\n

S_132 1 S_4 1 S_118 1 S_74 1 S_12 1 S_228 1 S_4 1 S_118 1 S_74 1 S_12 1 S_12 1 S_74 1 S_118 1 S_160 1 S_12 1 S_4 1 S_118 1 S_74 1 S_240 1 S_12 1 S_4 1 S_74 1 S_118 1

This node represents the homodimer of EGFR activated by TGFa on the early endosome. CCVs containing EGFR complexes rapidly release their coat and fuse with early endosomes.{[5]} Uncoating of coated vesicles by [[GAK/Epithelial|GAK]] and [[Hsc70/Epithelial|Hsc70]] allows for homotypic fusion in a Rab5-dependent and EEA1-dependent manner to form early endosomes{[, 8]}. \nTherefore, EGFR_EGFR_TGFa_End is activated by ([[EGFR_EGFR_TGFa_CCV/Epithelial|EGFR_EGFR_TGFa_CCV]] AND [[EEA1/Epithelial|EEA1]] AND [[Rab5/Epithelial|Rab5]] AND [[PIP3_345]] AND [[Hsc70/Epithelial|Hsc70]] AND ([[Rabaptin_5/Epithelial|Rabaptin_5]] OR [[GAK/Epithelial|GAK]])). Since EGFR activated by TGFa in early endosomes will be recycled back to the plasma membrane as inactive EGFR monomers, EGFR_EGFR_TGFa_End is turned off if it was active in the previous time point.\n\n

*Rabaptin_5 is required for the fusion of CCVs with early endosomes.{[10]-p(1941)} \n<br>*Rabaptin_5 is recruited to early endosomes by Rab5.{[10]-p(1941)} \n\n

*CCVs undergo uncoating in a process mediated by auxilin (GAK) and Hsc70, which is essential for CCVs fusing with early endosomes.{[6]-p(351)}{[7]-p(31.8)} \n\n

*CCVs undergo uncoating in a process mediated by auxilin (GAK) and Hsc70, which is essential for CCVs fusing with early endosomes.{[6]-p(351)}{[7]-p(31.8)} \n<br>*GAK supports the uncoating of clathrin from CCVs.{[4]-p(641)} \n\n

*Activation of EGFR_Free with activation of EGFR_EGFR_TGFa_CCV AND EEA1 AND Rab5 AND PIP3_345 AND Hsc70 indicates TGFa recycling back to the cell surface, therefore turning off EGFR_EGFR_TGFa_End.\n\n

*For the association of EEA1 with the endosome membrane, the concomitant presence of both Rab5 and PIP3_45 is crucial.{[3]-p(3748)}\n\n

*EEA1 is required for the fusion between EE and CCVs.{[3]-p(3747)}\n<br>*EEA1 molecules could provide several binding sites that are sufficient to tether an incoming CCV to the early endosome.{[1]-p(112)} \n\n

*EGFR_EGFR_TGFa-EE is activated by EGFR_EGFR_TGFa_CCV, which represents dymerized and activated EGFR in a clathrin-coated vesicle.\n\n

*Rab5 is necessary on both CCVs and early endosomes for a fusion event to occur.{[3]-p(3745, 3746)} \n<br>*Rab5 promotes endosome fusion by recruiting cytosolic components of the fusion apparatus.{[2]-p(697)} \n<br>*Rab5 is required for targeting and fusion of endocytic vesicles to early endosomes.{[9]-p(27)} \n\n

S_66 1 S_210 1 S_74 1 S_115 1 S_192 1 S_70 1 S_11 1 S_139 1 S_41 1

ErbB3_Y1178 (Tyr_1178 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1178 (Tyr_1178 site of ErbB3) is activated upon receptor dimerization [].\n\n

ErbB3_Y1178 (Tyr_1178 site of ErbB3) is activated upon receptor dimerization []\n\n

S_99 1 S_91 1 S_20 1

S_55 1 S_22 1

PP2A is a negative regulator of Mek when it is ON [38, 45, 32, 35, 4, 61, 34, 11, 29]. Pak activates Mek [55, 23, 44, 2, 37] and is required, but not sufficient for Mek activity [54, 51, 2], however, reference [] shows that the presence of Pak is required for PDGF stimulation, not EGF. Therefore, PAK is in an AND with the Raf pathway, but the Raf pathway without PAK is sufficient to activate MEK without PAK activity. Raf can activate Mek [15, 65, 64, 19, 7, 8, 52, 46, 48, 25, 6, 13, 27, 50, 36, 63, 42, 23, 33, 40, 10, 56, 16, 57, 26, 41, 5, 24, 58, 2]. Tpl2 can as well [21, 52, 3, 40, 61, 60, 49, 62, 14], and Tpl2 is OR with Raf [49, 62, 14].\nMekk1 [18, 61, 47, 60], Mekk2 [22, 52, 40, 61], and Mekk3 [61, 40] can all activate Mek. In addition to it's ability to phophorylate Mek, Mekk1 is thought to be a scaffold that brings Raf + Mek + Erk together, so we are putting Mekk1 AND with Raf. Since the mechanism of Mekk2 and 3 are not clear, we are making them similar to Mekk1, so they are both OR to Mekk1.\n\n

*Mekk2 and Tpl2 activate Erk via Mek {[22]-p(33), [52]-p(822)}\n<br>*Mekk1-3 activate MEK1/2 {[40]-p(2-Fig. 1)} -NOTE: we're not showing Mekk1 as an upstream of MEK\n<br>*Mekk2,in vitro, phosphorylates Mek and Sek1 {[61]-p(68)}\n\n

*Activation of PAKs by Cdc42 and Rac may be initiated to phosphorylate Mek {[55]-p(3), [23]-p(482)}\n<br>*Pak activates Raf and Mek {[44]-p(2-Fig. 1), [2]-p(2)}\n<br>*Pak phosphorylates Mek on Ser298 in a region that mediates the interation of MEK with Raf {[54]-p(3)}\n<br>*Mek contains 4 phosphorylatable sites that are targets for autophosphorylation, ERK1/2, or PAK {[61]-p(56)}\n<br>*Pak synergizes with Mek to stimulate MKK and Erk {[61]-p(71)}\n<br>*Pak phosphorylates Mek {[37]-p(1)}\n<br>*MEK is a PAK substrate {[51]-p(759)}\n\n

*Raf as an upstream of Mek {[15]-p(2-Fig. 1), [65]-p(3), [64]-p(2-Fig. 1), [19]-p(5-Fig. 1), [7]-p(3-Fig. 1), [8]-p(1), [52]-p(822), [46]-p(2-Fig. 1), [48]-p(3), [25]-p(1)}\n<br>*Mek is stimulated,activated by Raf {[6]-p(7), [13]-p(1), [27]-p(5-Fig. 1), [50]-p(1), [36]-p(1), [63]-p(161), [42]-p(3-Fig. 2), [23]-p(482), [33]-p(41-Fig. 6), [40]-p(2-Fig. 1)}\n<br>*Raf activates Mek1 {[10]-p(7)}\n<br>*MEK deactivated by PP2A can be reactivated by Raf {[38]-p(105)}\n<br>*All Raf family members can activate and phosphorylate MKK1/2 {[39]-p(2), [35]-p(7), [12]-p(1)}\n<br>*Raf phosphorylates Mek1/2 {[56]-p(7), [16]-p(2), [57]-p(1), [26]-p(276), [41]-p(3), [5]-p(187-Fig. 1), [24]-p(322)}\n<br>*Raf phosphorylates Mek at both sites (Ser218,222) {[61]-p(56), [47]-p(2)}\n<br>*Mek activation requires internalization of active Raf. {[31]-p(1)}\n<br>*Raf phosphorylates and activates Mek1/2 {[58]-p(1), [2]-p(1)}\n<br>*MEK is dually phosphorylated by Raf on two serines. {[20]-p(2)}\n<br>*Mek is activated by Raf, which is believed to be activated by binding to GTPRas. {[28]-p(1)}\n<br>*Raf activates Mek. {[28]-p(2), [17]-p(357)}\n<br>*Raf promotes phosphorylation of Mek, which in turn is required to activate Erk by phosphorylation. {[11]-p(1)}\n\n

*PP2A is an inhibitor of MEK {[38]-p(105)}\n<br>*PP2A can dephosphorylate MEK1 and ERK-family kinases {[45]-p(3), [32]-p(1), [35]-p(1), [4]-p(428)}\n<br>*PP2A and PP1 can inactivate ERK1/2 and MEK1/2 {[61]-p(80)}\n<br>*PP2A activation results in dephosphorylation and inactivation of MEK {[34]-p(2)}\n<br>*PP2A coordinates membrane recruitment of Ksr_Mek complex and the activation of Raf through dephosphorylation of a common 14-3-3 binding site. Both steps are required for activation of Mek and the subsequent activation of Erk. {[11]-p(1)}\n<br>*Mek and Erk are likely candidates for the inhibitory effect of PP2A, given that both kinases can be dephosphorylated and inactivated by PP2A in vitro, and that the inhibition of PP2A leads to Mek and Erk activation in vivo. {[29]-p(5)}\n

*Mekk1 phosphorylates Mek1/2 and Sek1 in vitro, Sek1 is preferentialy activated over Erk pathways {[61]-p(68)}\n<br>*Mekk1 phosphorylates MEK, but it's not sufficient to activate it alone {[47]-p(3)}\n<br>*Mekk1 and Tpl2 can phosphorylate MEK. {[60]-p(291)}\n<br>*Mekk1 can phosphorylate MEK. {[60]-p(291)}\n<br>*When Mekk1 is knocked out, signaling from both Erk and SAPK are diminished {[18]-p(40121)}\n<br>*Mekk1 may be a scaffold that brings together activated Raf + Mek + Erk. {[18]-p(40126)}\n\n

*Mekk3,in vitro, phosphorylates Mek,Sek1 and MKK3 {[61]-p(68)}\n<br>*Mekk1-3 activate MEK1/2 {[40]-p(2-Fig. 1)} -NOTE: we're not showing Mekk1 as an upstream of MEK\n\n

S_146 1 S_43 1 S_142 1 S_177 1 S_146 1 S_43 1 S_142 1 S_216 1 S_177 1 S_43 1 S_142 1 S_120 1 S_177 1 S_43 1 S_142 1 S_21 1 S_146 1 S_43 1 S_142 1 S_6 1 S_177 1 S_43 1 S_142 1

Nck [7, 8, 5, 1] OR TAK1 [9, 6, 2, 4, 3] activate NIK. Tpl2 only enhances the phosphorylation of NIK [9] therefore it will be an input but will fall out of the logic.\n\n

*NIK binds to Nck {[5]-p(378)} - not very clear in the paper\n<br>*NIK interacts with Nck {[8]-p(37), [7]-p(11)}\n<br>*Nck activates NIK {[6]-p(836)}\n<br>*NIK binds NCK and provides a link to JNK {[1]-p(5)}\n\n

S_85 1 S_221 1

*VPS4 is recruited by ESCRT_III.{[2, 3, 1]}\n\n

S_102 1

ErbB4_Y1056 (Tyr_1056 site of ErbB4) is activated when ErbB4 dimerizes. Therefore this node is ON when [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] OR [[ErbB2_ErbB4/Epithelial|ErbB2_ErbB4]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]] OR [[ErbB4_ErbB4/Epithelial|ErbB4_ErbB4]] is ON.\n\n

ErbB4_Y1056 (Tyr_1056 site of ErbB4) is activated upon receptor dimerization [1].\n\n

ErbB4_Y1056 (Tyr_1056 site of ErbB4) is activated upon receptor dimerization [1].\n\n\n

S_20 1 S_214 1 S_220 1 S_34 1

S_123 1

{ERK [10, 3, 5, 8, 11, 6, 9] OR SAPK [2, 1] OR p38 [5, 2, 1]} can activate MKPs, and they are in an AND with cAMP since cAMP induces MKP expression [, 1]. \n\n

*MKPs are upregulated upon Erk's activation and forms a negative feedback loop. {[10]-p(3), [3]-p(79)}\n<br>*MKP can be induced by Erk to inhibit SAPK and p38 signal transduction or, alternatively it can be induced by SAPK or p38 activation to dephosphorylate Erk {[5]-p(5)}\n<br>*Erks phosphorylate and activate MKP-3, a cytosolic MKP {[8]-p(484)}\n<br>*Erk is necessary for the stimulation of MKP-1 mRNA expression {[11]-p(4)}\n<br>*Erk2 activates MKP3 by direct binding {[6]-p(9)}\n<br>*Erk2 binding is accompanied by catalytic activation of MKP-3 in vitro and MKP-4 {[9]-p(187)}\n\n

*MKP can be induced by Erk to inhibit SAPK and p38 signal transduction or, alternatively it can be induced by SAPK or p38 activation to dephosphorylate Erk {[5]-p(5)} \n\n

*MKPS can be trascriptionally activated by cAMP {[4]-p(4)}\n<br>*cAMP stimulates MKPs {[11]-p(4)}\n\n

S_8 1 S_188 1 S_100 1 S_188 1 S_234 1 S_188 1

Gbg_q is an idealized Gbg that specifically binds Gaq. Gbg_q is activated by the GPCR a1-AR when it is associated with Gaq (i.e., when both Gaq and Gbg_q are OFF). It is deactivated when Gaq is GDP-bound (OFF) unless they are both OFF and alpha-q_R is ON. If Gaq is ON, then Gbg_q is separated and is ON. {[8, 1, 9, 6, 7, 3, 2]} \n\n

S_24 1 S_7 1 S_148 1 S_7 1

EGFR_T654 (Ser_654 site of EGFR) is phosphorylated (hence activated) by PKC.\n\n

PKC phosphorylates EGFR T654 [1].\n\n

S_240 1

Mekk4 is activated by Cdc42 OR Rac [2]. \n\n

*Rac activates Mekk4 {[2]-p.828}\n\n

*Cdc42 activates Mekk4 {[2]-p.828}\n\n

S_132 1 S_160 1

DOCK180 is activated by Crk[5, 4, 2, 9, 7] AND Cas[11, 5, 9, 7, 2] AND the recruitment to the plasma membrane by PIP3_345 [4, 8].\n\n

*DOCK180 is recruited by phosphorylated Cas which leads to activation of Rac {[11]-p(6)}\n<br>*Cas/Crk couple to DOCK180 which faciliates Rac activation {[5]-p(231), [9]-p(12)} \n<br>*DOCK180 is one of hte downstream effectors of the integrin-Cas signaling cascade. {[7]-p(3)}\n<br>*DOCK180 links Cas-Crk interactions to Rac {[2]-p(4)}\n\n

*Cas/Crk couple to DOCK180 which faciliates Rac activation {[5]-p(231)}\n<br>*DOCK180 is phosphorylated and bound to CrkII when stimulated with integrin. {[7]-p(1)}\n<br>*Binding of CrkII to DOCK180 is required for hyperphosphorylation of p130Cas. {[7]-p(1)}\n<br>*DOCK180 links Cas-Crk interactions to Rac {[2]-p(4), [10]-p(1412)}\n<br>*Dock180 is bound by Crk {[4]-p(6357), [9]-p(12)}\n \n

*PIP3_345 was found to bind DOCK180 to translocate it to the plasma membrane {[4]-p(6358)}. The possibilities of PI3K-Rac cross talk opened up by this interaction not specified.\n<br>*In SOME WAY PIP3_345 can bind to a basic region at the C-terminus of Dock180, albeit without any effect on Rac-GTP loading {[6]-p(3)}\n

S_153 1 S_74 1 S_129 1

The main activator of Crk is Cas [16, 10, 7, 3, 12, 13, 9, 5, 6, 14]. It appears that Fak OR Src phosphorylation of paxillin is necessary to localize Crk for subsequent signaling through DOCK180 [, 14, 17], so they are necessary for Crk activation. PTPPEST can block Cas/Crk/DOCK180 signaling by dephosphorylating paxillin [], so PTPPEST will be a negative (dominant) regulator of Crk.\n\n

*Dephosphorylation of Cas via PTP-PEST is necessary for modulation of Crk binding. {[14]-p(5)} \n \n

*Phosphorylation of Cas by FAK can result in the recruitment of Crk and Nck adaptor proteins {[16]-p(12), [10]-p(1)} \n<br>*Phosphorylation of Cas can result in the recruitment of Crk {[7]-p(6)}\n<br>*Cas binds Crk {[9]-p(279)}\n<br>*Cas is a major binding protein for Crk {[3]-p(1)}\n<br>*Integrin stimulation induces the binding of Cas to CrkII. {[12]-p(2)}\n<br>*Integrin-dependent phosphorylation of Cas often results in the establishment of the Cas-Crk complex {[2]-p(4)}\n<br>*Crk SH2 binds to Cas {[13]-p(7)} \n<br>*FAK dependent Cas-Crk coupling is required for induction of cell migration. Cas-Crk co-overexpression enhanced cellular motility, in a process requiring Rac GTPase, and Crk SH2 domain. {[5]-p(114)}\n<br>*Cas/Crk complexes recruit DOCK180 and Rac leading to GTPase activation. {[14]-p(5), [6]-p(1411)}\n<br>*Cas recruites Crk to focal adhesions, and Crk in turn recurites DOCK180. {[14]-p(5)}\n<br>*persistent Rac activation in cells promoted sustained Cas/Crk coupling. {[14]-p(5)}\n<br>*Crk uncouples from Cas without apparent changes in FAK activity and Cas tyrosine phosphorylation. {[14]-p(5)}\n<br>*Crk phosphoyrlation is necessary for Crk translocation. {[14]-p(5)}\n<br>*Fak and/or Src tyrosine kinases appear to serve as positive amplifiers of Cas/Crk assembly through phosphorylation of Cas. Signal amplification then results from the docking of multiple Crk molecules to Cas, which in turn leads to the recruitment of various effectors. {[14]-p(5)}\n<br>*Dephosphorylation of Cas via PTP-PEST is necessary for modulation of Crk binding. {[14]-p(5)}\n\n

S_129 1 S_244 1 S_135 1 S_75 1

Grb2 is a positive regulator and is necessary for the recruitment of Gab1 to the EGF receptor {[11, 12, 9, 2, 8, 6]. EGFR is a necessery positive regulator of Gab1 {[3, 10, 1, 4, 11, 8]}. Therefore all localizations and heterodimers involving EGFR will be activators (in an OR relationship) of Gab1. PIP3_345 is also a positive regulator on the recruitment level, but only to prolong the activation of Gab1 {[14, 18, 6]}. Therefore, if Gab1 is OFF, EGFR (all of its heterodimers and localizations) AND Grb2 will turn it ON. If Gab1 is ON, EGFR (all of its heterodimers and localizations; except for Lysosome) AND PIP3_345 will keep it ON. In addition, SHP2 is a dominant negative regulator {[7, 4, 12, 16, 8]}.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*SHP2 can dephosphorylate Gab1 {[7]-p(2), [4]-p(5)}\n<br>*SHP2 can dephosphorylate Gab1 to inhibit the signalling from Gab1 to PI3K {[4]-p(5,7), Fig.4}\n<br>*SHP2 regulates phosphorylation of another site on Gab protein. {[4]-p(5)}\n<br>*Gab1 is physically associated with Shp2 in a tyrosine phoshphorylation dependent fashion. {[12]-p(1)}\n<br>*It is highly likely that Gab1 and EGFR are SHP2 physiological substrates {[16]-p(7)}\n<br>*Shp2 appears to specifically dephosphorylate Gab1-associated p90 and to a minor extent Gab1 itself. {[2]-p(8), [8]-p(5351)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Grb2 binds directly to Gab1 through its C-SH3 domain {[11]-p(2)}\n<br>*Grb2 is OR in its ability to stimulate Gab1 or Sos {[11]-p(4)}\n<br>*Grb2 binds to Gab1. {[12]-p(1), [9]-p(1)}\n<br>*Grb2 can bind to Gab1 via two mechanisms: through SH3 interaction of Gab1, or Sh2 recognition of a residue. {[2]-p(7)}\n<br>*In response to EGF, Gab1 is recruited by Grb2 in the vicinity of EGFR and becomes phosphorylated. This causes the activation of SHP2 and PI3K {[8]-p(5350)}\n

*As mentioned below, EGFR phosphorylates and activates Gab1. Therefore all localizations and heterodimers involving EGFR will be activators of Gab1.\n<br>*Gab1 is phosphorylated by EGFR at Tyr_527 and Tyr_659 {[3]-p(7), Fig.10} \n<br>*Tyrosyl phosphorylation of Gab1 promoted by EGF. {[10]-p(5)}\n<br>*Gab1 as a candidate for mediating the activation of PI3K by the EGFR {[1]-p(5)}\n<br>*In the EGFR pathway, Gab1 phosphorylation occurs via a mechanism involving an additional scaffolding adaptor, FRS2. Upon receptor activation, FRS2 becomes tyrosine phosphorylated and binds to Grb2,which,in turn recruits Gab1. {[4]-p(3)}\n<br>*Gab1 phosphorylation is induced by EGFR which results in the recruitment of PI3K {[11]-p(4)}\n<br>*Gab1 is tyrosine phosphorylated in response to EGFR activation. {[6]-p(1455)}\n<br>*Gab1 associates with EGFR in vivo and in vitro; overexpression of Gab1 potentiates EGF_induced activation. {[6]-p(1448)}\n<br>*Gab1 binds directly to EGFR {[6]-p(1449)}\n<br>*Gab1 translocates to the membrase upon EGFR stumulation in a PI3K dependent fashion. {[6]-p(1451)}\n<br>*In response to EGF, Gab1 is recruited by Grb2 in the vicinity of EGFR and becomes phosphorylated. This causes the activation of SHP2 and PI3K {[8]-p(5350)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*PH domain of Gab1 binds to PIP3_345 {[14]-p(2,4)}\n<br>*Expression of PTEN inhibits movement of Gab1 to the plasma membrane by dephosphorylation of PIP3_345 since Gab1 binds this phospholipid in its translocation to the membrane. {[18]-p(36)}\n<br>*Gab1 specifically binds to PIP3_345 and is required for activation of Gab1-mediated enhancement of EGFR signaling. {[6]-p(1448)}\n<br>*PTEN dephosphorylates PIP3_345, which inhibits EGF signaling and translocation of Gab1 to the plasma membrane. {[6]-p(1448)}\n<br>*Gab1 binds primarily to PIP3_345, and can target Gab1 to the plasa membrane in response to EGF stimulation. {[6]-p(1449)}\n<br>*PIP3 allows Gab1 to bind to EGFR after the initial activation {[6]-p(1457)}\n<br>*Gab1 binds significantly more strongly to PIP3_345 then to PIP2_34 and PIP2_45. {[6]-p(1452)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_19 1 S_154 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_198 1 S_154 1 S_74 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_198 1

Gaq turns on PLC_B [14, 5, 2, 7, 3, 9], and after PLC_B opens up (from the Gaq stimulation), Gbg_i can also activate it [9, 8]. Gbg_i cannot activate on it's own [12, 14, 13, 10]. Thus, if PLC_B is ON AND Gbg_i is ON, PLC_B will stay ON [10, 13]. PKA is negative [12, 1], but only if Gaq is off. So PKA is dominant to Gbg_i [13], but not Gaq [13].\n\n

*PKA phosphorylates PLCb at a serine residue and inhibits it {[12]-p(2)} \n<br>*PKA can phosphorylate and inhibit b-isoforms of PLC {[1]-p(164)}\n<br>*Phosphorylation of PLCb by PKA and PKC link the b-isoforms to heterologous and homologous receptor pathways that modulate phosphoinositide/Ca signals {[13]-p(1302)}\n<br>*PKA phosphorylates and inhibits PLCb activation by Gbg and partially the activation by Gaq. {[13]-p(1302)}\n

*PLCb is activated by Gaq {[14]-p.9(289), [5]-p(4), [7]-p(670), [9]-p(556), [8]-p(1940), [11]-p.890}. \n<br>*Great review on upstreams of PLC {[13]}-PLCb is downstream of G-protein subunits [p.1313] \n<br>*Activation of PLCb is stimulated by Gaq {[2]-p(2), Fig. 1}\n<br>*Gbg and Gaq subunites are required for efficient PLCb activation {[6]-p(765)}\n<br>*Gaq activates PLCb, but also opens it up for Gbg to stimulate too. {[10]-p(284)}\n<br>*Gaq stimulates PLC {[3]-p(1)}\n<br>*Ga first binds GTP to PLCb and then Bgb or Ga, or both bind to GTP-PLCb and increase its activity {[13]-p(1299)} (strong model)\n<br>*Contradictory model: PLCb may be activated by Gaq ot its associated Gbg, but not Gbg arising from Gi/o {[13]-p(1300)}\n<br>*Ga stimulate PLCb but fail to stimulate PLCg {[13]-p(1299)}\n<br>*RGS interact most effectively with Gaq and block activation of PLCb {[13]-p(1301)}\n\n

S_222 1 S_155 1 S_133 1 S_7 1 S_7 1

There are many different RGS's, each with different mechanisms of regulation. In the model, RGS will be an idealized version of RGS. PIP3_345 keeps RGS associated with the membrane [3, 4] and is a negative regulator [2, 5, 3]. RGS's may also bind to GPCR to dictate specificity in RGS-Ga interactions, but this binding is independent of the activation state of the GPCR [4] so it will be left out. CaM relieves the PIP3_345 mediated inhibition of RGS [1, 2, 3], and it is dominant over PIP3_345. After CaM activation, the idealized RGS is active to all Ga's. \n\n

*Activity of RGS can be restored by CaM {[1]-p(3), Fig. 2} \n<br>*Ca/CaM binds to RGS, but doesn't inhibit its GAP activity {[2]-p(534)}\n<br>*The Ca/CaM complex binds to RGS and relieves the PIP3-mediated inhibition, restores GAP activity of RGS, and accelerates the hydrolysis of GTP on Ga, which causes the GDP-Ga re-assiciation with Gbg. {[3]-p(4)}\n

*PIP3_345 binds to RGS to inhibit its GAP activity,therefore IP3 is produced again {[2]-p(534)}\n<br>*RGS protein are inhibited by PIP3_345 {[5]-p(3)}\n<br>*In the resting state, PIP3_345 binds to RGS to inhibit its GAP activity {[3]-p(4)}\n<br>*RGS is constitutively associated with the membrane (through PIP3_345 binding?). {[4]-p(548), [3]-p(167)}\n

S_3 1 S_74 1

This node represents the homodimer of EGFR activated by TGFa on the cell surface. EGFR_EGFR_TGFa_PM is activated by [[TGFa]] AND [[EGFR_Free/Epithelial|EGFR_Free]], unless EGFR_T654 is active. [[ErbB2_Free/Epithelial|ErbB2_Free]] is a negative regulator of EGFR_EGFR_TGFa_PM (dominant over TGFa AND EGFR_Free). EGFR_EGFR_TGFa_PM localizes to EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCP will turn EGFR_EGFR_TGFa_PM off if it was on in the previous step.\n\n

*TGFa is released from the receptor in early endosomes, leading to receptor dephosphorylation and recycling back to the plasma membrane. TGFa does not cause significant degradation and downregulation of EGFR. {[6]-p(689)}\n<br>*TGFa binds to EGFR.{[8]-p(42)}{[1]-p(12)}{[5]-p(1528)}\n\n

*EGFR_EGFR_EGF_PM is activated by EGFR_Free, which represents unliganded EGFR on the cell surface.\n\n

Is ErbB2 is the preferred dimerizing partner for all ErbBs [] -- ErbB2_Free will be a negative regulator of EGFR_EGFR_EGF_PM.\n\n

S_41 1 S_64 1 S_149 1 S_30 1 S_117 1 S_157 1 S_30 1

EGFR_Y920 (Tyr_920 site of EGFR) is phosphorylated (hence activated) by Src. Because this is an EGF_dependent event [7], EGF_activated EGFR homodimer also has to be active.\n\n

*Src phosphorylates EGFR on Y891 and Y920 (in vitro, []), as well as Y845 and Y1101 ([2],<cite>Jorrison</cite>-p.39,[3]). Y845 is phosphorylated by Src in vitro and vivo ([],<cite>Jorrison</cite>-p.39)\n<br>*Src is activated in response to growth factors such as PDGF, which induces PDFGR autophosphorylation {[6]-p(4)}\n<br>*Src kinase activity is required for phosphorylation of other tyrosine residues {[5]-p(2)}\n\n

S_244 1 S_52 1

AP2 is recruited by [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]], [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]],[[CIN85]],[[PIP2_45]],[[PIP3_345]],[[Eps15/Epithelial|Eps15]],[[Epsin/Epithelial|Epsin]] or [[Hip1R/Epithelial|Hip1R]].{[5, 6, 3, 1, 7, 12, 8, 4]}\n\n

* Ligand activated EGFR recruits several coat adaptors, such as adaptor protein 2 (AP2) and Eps15. {[4]-p(349)}{[5]-p(540)}\n\n

*AP2 is activated by PIP2_45 and PIP3_345.{[10]-p(5,10-11)} {[1], p-(4)}\n<br>*AP2 is recruited to the plasma membrane through its binding to PIP2_45.{[12]-p(5,10-11)} {[8]-p(418)} \n\n

*Hip1R recruits clathrin and AP2 to the plasma membrane.{[7], p-(312)}\n\n

*AP2 is activated by PIP2_45 and PIP3_345.{[10]-p(5, 10-11)} {[1], p-(4)}\n\n

*Eps15 appears to act as a scaffolding protein and clusters AP2 appendages. {[6]-p(31.9)}{[3], p-(304)}{[1], p-(4)}\n\n

*AP2 can be recruited through CIN85.{5[11]-(911)} \n\n

*Epsin recruits AP-2 directly or indirectly via Eps15.{[1], p-(6)}\n<br>*AP2 binds to the endocytic accessory proteins epsin, CALM and Eps15.{[8], p-(418)}\n\n

S_118 1 S_105 1 S_36 1 S_157 1 S_225 1 S_245 1 S_74 1 S_52 1

Rac is defined ON when it is localized at the plasma membrane and GTP loaded.\nRalBP1 [23, 52, 62] are GAPs and negative regulators for Rac. RhoGDI is also a negative regulator of Rac [70, 37, 71, 1, 22, 45] because it sequesters GDP/GTP bound Rac. Cell attachment to ECM required for Rac to be localized at the plasma membrane, therefore, ECM AND Integrins a necessary for Rac activation [10].\nPAK [66] is able to break up Rac-RhoGDI complex and stop the negative regulation of Rac by RhoGDI. The activation of Rac is done by RasGRF [61, 46, 6, 14] OR Tiam [69, 54, 72, 52, 60, 20, 35, 14] OR Pix_Cool [11, 34, 52, 20, 49, 21, 58] OR DOCK180 [8, 60, 71, 19, 56, 51, 41, 14, 17, 27]. However, despite the fact that many of the details haven't been full discovered, the activation mechanism of Rac by Pix/Cool appears to be much more complicated than the previously discussed Rac activators. In addition to the requirement of cell attachment, there are three different scenarios under which Pix_Cool modulates the activity of Rac. First, when Gbg_i [12] AND PAK1 are 'ON' PIX only activates Rac if both Cdc42 AND Rac are 'Off'. Second, when Gbg_i is inactive, Pix_Cool activates Rac only if Rac was previously inactive, and Cdc42 is active. In addition this step also requires the activity of Cdc42. Finally, when Gbg_i is active (and PAK is inactive), Pix_Cool activates Rac only when Rac was previously inactive, and RhoGDI and all other positive regulators are also inactive. [28, 48, 58, 12] (Note that due to incomplete biological data, some of the logic of the mechanism had to be adjusted in the context of the whole model.)\n\n

*Tiam is a GEF for Rac {[60]-p(2), [52]-p(5), [69]-p(10)}\n<br>*Tiam is a Rac-specific GEF. {[72]-p(9)}\n<br>*Tiam shows exchange activity towards Cdc42, Rac and Rho, in vitro, but only Rac in vivo. {[72]-p(2)}\n<br>*Tiam activates Rac {[54]-p(730), [14]-p(174)}\n<br>*Tiam1 is activator of Rac {[20]-p(583, 584)}\n<br>*Tiam1 is Rac1 exchange factor {[35]-p(132), [72]-p(1589)}\n\n

*DOCK180 is recruited by phosphorylated Cas which leads to activation of Rac {[60]-p(6)}\n<br>*Cas/Crk couple to DOCK180 which faciliates Rac activation {[2]-p(231), [8]-p(280)}\n<br>*DOCK180 links Cas-Crk interactions to Rac {[56]-p(4)}\n<br>*Dock180 binds and activates Rac, but not Cdc42 {[19]-p(6357)}\n<br>*DOCK180 increases Rac-GTP loading {[4]-p(3)}, but it can't bind GDP-Rac\n<br>*Dock180 is a Rac GEF {[25]-p(7933), Fig. 1}, even though it lacks the Dbl-homology/pleckstrin-homology tandem domains characteristic of conventional Rho-family GEFs {[49]-p(574)}\n<br>*DOCK180 is a Rac1-specific GEFs {[35]-p(129), [14]-p(177), [17]-p(23388)}\n<br>*DOCK180 is a specfic GEF for Rac {[38]-p(3476)}\n<br>*DOCK180/ELMO complex work as a Rac-specific GEF {[51]-all, [27]}\n\n

*apparently can work as a Rac GEF {[52]-p(7)}\n<br>*PAK interacts with exchange factor PIX for Rac, stimulating it to further activate GTPases. {[11]-p(2)}\n<br>*Pix is a positive regulator of Rac. {[34]-p(1-Fig. 1)}\n<br>*a-Pix/Cool-2 is activator of Rac {[20]-p(583)}\n<br>*PIX is a conventional Rac GEF {[49]-p(574)}\n<br>*PIX can activate Rac1 and Cdc42 {[21]-p(567), [58]-p(1)}\n

*RalBP1 is a GTPase-activating protein for Rac1 and Cdc42 {[23]-p(162, Fig. 4), [52]-p(8)}\n<br>*RalBP1 can potentially regulate Rac and Cdc42 {[62]-p(4)}\n\n

S_40 1 S_222 1 S_21 1 S_200 1 S_23 1 S_160 1 S_21 1 S_1 1 S_151 1 S_161 1 S_160 1 S_132 1 S_200 1 S_23 1 S_222 1 S_160 1 S_200 1 S_23 1 S_132 1 S_161 1 S_200 1 S_23 1 S_88 1 S_160 1 S_1 1 S_200 1 S_23 1 S_88 1 S_160 1 S_160 1 S_88 1 S_88 1 S_160 1 S_151 1 S_200 1 S_23 1 S_88 1 S_160 1

RasGrf's and RasGrp's have different tissue distributions with differing amounts of information available on each. Therefore this node is a composite generalization of RasGrf's and RasGrp's designed to have a connection between calcium and Ras. Its inputs are CaM, DAG, and Cdc42. Based on the composite data, the logic will be that Cdc42 is a dominant negative regulator when Cdc42 is off [7], DAG OR CaM can activate RasGRF/RasGRP [3, 11]. \n\n

*RasGRF contains an IQ motif that is regulated by CaM {[4]-p(160), [7]-p(1), [11]-p(340)}\n<br>*RasGRF is Ca/calmodulin dependent {[10]-p(2), [3]-p(52, 53)}\n

S_18 1 S_132 1 S_3 1 S_132 1

ErbB4_Y1188 (Tyr_1188 site of ErbB4) is activated when ErbB4 dimerizes. Therefore this node is ON when [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] OR [[ErbB2_ErbB4/Epithelial|ErbB2_ErbB4]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]] OR [[ErbB4_ErbB4/Epithelial|ErbB4_ErbB4]] is ON.\n\n

ErbB4_Y1188 (Tyr_1188 site of ErbB4) is activated upon receptor dimerization [1].\n\n

ErbB4_Y1056 (Tyr_1188 site of ErbB4) is activated upon receptor dimerization [1].\n\n

S_20 1 S_220 1 S_214 1 S_34 1

ErbB3_Y1257 (Tyr_1257 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1257 (Tyr_1257 site of ErbB3) is activated upon receptor dimerization [].\n\n

S_20 1 S_91 1 S_99 1

PLA2 is defined as ON when it is activated AND localized. Ca OR (PIP2_45 AND PIP3_345) is required to localize PLA2 to the membrane [6, 9, 8]. Those three are AND with Erk OR CaMK, which provide the activating phosphorylation after it is localized [8, 3, 7, 4, 1, 6, 5]\n\n

*Erk increases the activity of PLA2 {[8]-p(798), [3]-p(89)}\n<br>*Erk2 phosphorylates and regulate the activity of PLA2 {[7]-p(461)}\n<br>*Erk is an upstream regulator of PLA2 {[4]-p(2-Fig. 1)}\n<br>*Phosphorylated Erk activates PLA2 {[1]-p(2), [5]-p(1188)}\n\n

*The activation of PLA2 can be mediated by several signals, such as phosphorylation cascades, intracellular Ca elevations, and perhaps PIP2_45 levels {[9]-p(180)} \n<br>*Ca activates PLA2 {[8]-p(796), Fig. 1}\n<br>*An increase in intracellular Ca concentrations promotes binding of Ca to hte C2 domain and then allows cPLA2a to translocate from cytosol to the preinuclear region including the Golgi ap.m ER, and nuclear envelope {[6]-p(2)}\n<br>*iPLA2 is regulated by Ca, but it's not required {[2]-p(1)}\n

S_118 1 S_234 1 S_74 1 S_74 1 S_118 1 S_68 1 S_68 1 S_229 1 S_234 1 S_229 1

B_Arrestin [3, 2] and PKA [2] are positive regulators of PDE4; Erk is a negative regulator [3, 2]. \nB_Arrestin is required for the recruitment of PDE4 [3] to the GPCR and is therefore necessary for PDE4 activation.\nPKA is dominant to Erk [2, 3].\n\n

*b-arrestin can form a complex with PDE4 that is then recruited to attenuate the activity of PKA responsible for phosphorylating the B-AR, presumably by lowering local cAMP levels. Thus the recruitment PDE4 serves to desensitize the switched coupling of b-AR to activation of Gi and hence to Erk. The cell-type-specific expression of appropriate PDE4 isoforms can thus serve to regulate the switch of coupling of the b-AR from Gs to Gi {[2]-p(1186)}\n\n<br>*b-arrestin recruits PDE4 to the active GPCRs where it degrades cAMP {[3]-p(130, 131)}\n\n

*ERK phosphorylation of long PDE4 causes inhibition of PDE4. Thus Erk inhibition of PDE4 causes a rise in cAMP level. {[2]-p(1188), [3]}\n\n

*PKA phosphorylates PDE4 to overcome the effect of phosphorylation by Erk {[2]-p(1188), [3]}\n\n

S_95 1 S_234 1 S_133 1 S_95 1

EGFR_Y1148 (Tyr_1148 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer).\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [, 1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

S_194 1 S_214 1 S_157 1 S_99 1 S_52 1 S_195 1

S_24 1 S_22 1

EGFR_Y992 (Tyr_992 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer). SHP2 deactivates EGFR_Y992.\n\n

*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

*It is highly likely that Gab1 and EGFR are SHP2 physiological substrates {[3]-p(7)}\n<br>*SHP2 can partially dephosphorylate EGFR {[3]-p(3)}\n<br>*SHP dephosphorylates PDGFR on specific tyr res. involved in Ras-GAP binding, thus decreasing Ras-GAP activation and potentiating Ras signalling {[]-p(3)}\n<br>*SHP2 dephosphorylates EGFR at a site where p120RasGAP binds, therefore inhibiting the regulation by EGFR {[2]-all}\n\n

S_99 1 S_198 1 S_170 1 S_195 1 S_198 1 S_170 1 S_170 1 S_198 1 S_170 1 S_194 1 S_198 1 S_170 1 S_52 1 S_198 1 S_170 1 S_157 1 S_198 1 S_170 1 S_214 1 S_198 1 S_170 1

Tab_1_2 is activated by Trafs [3, 4]. p38 is a dominant negative regulator of Tab_1_2 [2, 1]\n\n

*TRAF6 binds MEKK1 and TAk1 via Tab2 {[3]-p(5)}\n<br>*Tab2 is recruited by TRAF6 to connect TAK1 and TRAF6 {[4]}\n\n

*It was reported that the association of Tab1 and p38alpha negatively regulates TAK1 kinase activity by phosphorylating Tab1 at Ser423 and Thr431 {[2]-p(7360, 7367)}\n<br>*TAB1/2 are phosphorylated and inhibited by p38 {[2]-p(7367)}\n<br>*Tab1 and perhaps Tab2 are phosphorylated and negatively regulated by p38alpha {[1]-all}\n

S_123 1 S_8 1

PKA [10, 1, 13] OR PAK [7, 18, 22, 1, 21, 10, 19, 8] can turn OFF MLCK. We have them as dominant. When both of those negative regulators are OFF, Erk [14, 2, 11, 20, 9, 17, 15, 6] OR CaM [5, 7, 16, 12] will turn MLCK ON. \n\n

*Ca-CaM complex activates MLCK, which phosphorylates the 20-dKa MLC {[12]-p(1), [7]-p(762)}\n<br>*MLCK is regulated by Ca2+-calmodulin. {[5]-p(1)}\n<br>*MLCK is CaMK dependent kinase regulated by Ca {[16]-p(2)}; Although Ca sensitivity of MLCK differs for different smooth muscles {[16]-p(2)}-->smooth muscle\n<br>*MLCK binds to and is activated by the CaM complex {[1]-p(163)}\n \n

*ERK signaling leads to MLCK activation {[14]-p(6), [9]-p(6), [15]-p(59)}\n<br>*Erk directly phosphorylates and activates MLCK {[11]-p(13), [20]-p(461, 466), [2]-p(234)}\n<br>*v-Src-induced Erk/MAPK activity stimulates MLCK activation {[17]-p(6)}\n<br>*Erk phosphorylates MLCK to promote contractility {[6]-p(1326)}\n<br>*Erk phosphorylates MLCK {[2]-p(234)} \n\n

*PKA can phosphorylate and inactivate myosin light chain kinase {[13]-p(577)}\n<br>*PKA can phosphorylate MLCK and negatively regulate the interaction of CaM with MLCK {[1]-p(164), [10]-p(275, 276)}\n--> sounds dominant from {[10]} \n

S_234 1 S_21 1 S_133 1 S_21 1 S_133 1 S_3 1 S_21 1 S_133 1 S_21 1 S_133 1

This node represents EGF_activated homodimer of EGFR localized in clathrin-coated pits. Ubiquitinated EGFR is sorted into CCPs by binding to [[AP2/Epithelial|AP2]], [[Eps15/Epithelial|Eps15]] or [[Epsin/Epithelial|Epsin]].([6, 9, 12, 14, 8, 7, 3]) Furthermore, activated [[Rab5/Epithelial|Rab5]] is important for sequestering ligands into CCPs, and [[PIP2_45]] and [[Clathrin/Epithelial|Clathrin]] are necessary for the invagination of CCP.{[, 4]} Therefore, EGFR_EGFR_EGF_CCP is activated by ([[EGFR_Ub/Epithelial|EGFR_Ub]] AND PIP2_45 AND Clathrin AND Rab5 AND (Eps15 OR Epsin OR AP2)). When CCPs are pinched off from the plasma membrane and CCVs are created, [[EGFR_EGFR_EGF_CCV/Epithelial|EGFR_EGFR_EGF_CCV]] will replace EGFR_EGFR_EGF_CCP. Therefore, EGFR_EGFR_EGF_CCV acts as a negative regulator of EGFR_EGFR_EGF_CCP.\n\n

PI(4,5)P2 is enriched in the plasma membrane and is required for the invagination of CCPs.{[4]-p(31.25)}\n

*Clathrin is assembed to form CCPs and cargo (EGFR) is recruited.{[5]-p(312)}\n\n

*Endocytosed receptors are sorted into CCPs by interaction with the clathrin-binding AP-2 complex or by binding to other adaptor proteins, which in turn interacts with the clathrin heavy chain and/or AP2.{[6]-p(610)}{[9]-p(565)} {[12]-p(12111)}{[14]-p(793)}{[8]-p(R49)} \n\n

*Eps15 and epsin recruits(activates) EGFR to CCPs. {[6]-p(610)}{[]-p(171)}\n<br>*Eps15 is important for ligand-induced EGFR internalization and it is thought to recruit ubiquitylated receptors to CCPs.{[7]-p(3235)}\n\n

*Activaton of EGFR_EGFR_EGF_CCV results in removing (i.e., turns off) EGFR_EGFR_EGF_CCP.\n\n

* Eps15 and epsin recruits(activates) EGFR to CCPs. {[6]-p(610)}{[]-p(171)} \n\n

*Activated Rab5 is important for sequestering ligands into CCPs and subsequent fusion of vesicles with early endosomes.{[13]-p(184)}{[1]-p(110)}\n\n

S_174 1 S_29 1 S_36 1 S_81 1 S_192 1 S_183 1 S_118 1 S_52 1 S_29 1 S_225 1 S_52 1 S_118 1 S_183 1 S_81 1 S_192 1 S_29 1 S_159 1 S_52 1 S_183 1 S_81 1 S_192 1 S_118 1 S_29 1

EGFR can phosphorylate and activate PLC-g when the phospholipase is bound to phosphorylated Y992, Y1173, or Y1068 sites on EGFR [8, 6, 18, 21, 14, 2, 28, 31, 13, 19, 25, 18]. Note that EGFR is represented by the following variations of EGFR used in the model: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_LE, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End, EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4. PA [18, 26, 3] and AA [18, 26] also activate (independently) PLC_g. \n\n\n

* \n<br>* Same as EGFR_EGFR_EGF_PM\n\n

*PLCg is activated by PA and AA {[18]-p/23(303), [26]-p(766)}\n<br>*PLCg is activated by PA {[3]-p(43)}\n

* \n<br>* Same as EGFR_EGFR_EGF_PM\n\n

* Same as EGFR_EGFR_EGF_PM\n\n

*PLCg binds to autophosphorylated EGFR_Y992 and EGFR_Y1173 and is then phosphorylated by EGFR kinase [13, 19]-p.40\n<br>*The activation by EGFR requires that PLC_Binds to the autophosphorylated sites. [18]\n\n

*PLCg binds to autophosphorylated EGFR_Y992 and EGFR_Y1068 and is then phosphorylated by EGFR kinase [25]-p.284\n<br>*The activation by EGFR requires that PLC_Binds to the autophosphorylated sites. [18]\n\n

* Same as EGFR_EGFR_EGF_PM\n\n

*PLCg is activated by EGFR,then cleaves PIP2_45 into IP3 and DAG {[8]-p(1)}\n<br>*PLCg is a downstream of EGFR {[29]-p(4)}\n<br>*PLCg is activated by activated EGF receptor {[6]-p(7), [18]-p.14(294), [21]-p(29)}\n<br>*PLCg is phosphorylated by activated EGF receptor {[14]-p(2)}\n<br>*EGFR activation leads to plasma-membrane-restricted activation of the PLCg pathway {[2]-p(108), Fig. 1}\n<br>*PLC-g1 can form complexes with PDGFR or EGFR in vivo, which leads to its phosphorylation and increase in its enzymatic activity {[28]-p(1)}\n<br>*PLCg and PI3K is activated by GFRs {[31]-p(1306)}\n\n

* Same as EGFR_EGFR_EGF_PM\n\n

S_182 1 S_78 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_113 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_170 1 S_16 1 S_157 1 S_30 1 S_227 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1

WASP is an activator of Arp_2_3 [6, 11, 20, 8, 25, 21, 24, 1, 10, 9, 5, 13, 4]. When WASP is OFF, Arp_2_3 is OFF. [12]\n\n

*WASps are responsible for binding to Arp2/3 {[6]-p.2,[11]-p(10)}\n<br>*The COOH terminus of N-WASP binds the Arp2/3 complex and stimulates its ability to nucleate actin polymerization in vitro {[20]-p.170} \n<br>*The WH2 domain of Wasp binds Arp2/3 to a monomeric actin, promoting the nucleation of the new filament. {[12]-p(1)}\n<br>*WASP is key regulator of teh Arp2/3 complex {[8]-p(578), Fig. 4}\n<br>*Wasp/Scar family proteins are responsible for Arp2/3 complex activation {[22]-p(174),[1]-all}\n<br>*WASP binds to the Arp23 complex and enhance the nucleation activity of the complex {[21]-p(122),[16]-p(77)}\n<br>*WASP/SCAR/WAVE proteins activate the Arp2/3 complex {[24]-p(3471)}\n<br>*N-WASP activates the Arp2/3 complex {[10]-p(63), [5]-p.17115, [9]-p(5685), [13]-p(23380), [4]-p(881)}\n\n

S_38 1

\nErk is a negative regulator that inactivates Raf-1 [82, 30, 66]. Akt [40, 70, 77, 54, 42, 16, 79, 30, 48, 38] and PKA [30, 75, 76, 42, 77, 82, 85, 79, 77, 48, 66] are negatives, they are in an OR. All of the negative regulators generally inactivate Raf when it was already ON unless exeption is stated below.\n\nPP2a is necessary to dephosphorylate the inhibitory site on Raf when Raf was OFF [60, 46, 85, 15, 79, 43, 48]. Pak phosphorylates Raf and is required for the integrin-stimulated and anchorage-dependent activation of Raf, but doesn't seem to be sufficient to activate Raf without Src phosphorylation.[4, 71, 74, 6, 84, 35] Src [82, 79, 87] Src is also in an AND with Ras, which is necessary for the initial step of Raf activation [32, 11, 50, 86, 53, 57, 47, 76, 72, 85, 27, 80, 87, 48, 30]. RKIP phosphorylation (activation) is necessary for the Raf full activation, as well as phosphorylation by Src and PAK [31, 87, 49, 69]\nPA moves Raf to the membrane [44, 82], but it is not necessary or sufficient to activate Raf, so will fall out of the logic.\n\nRas is only necessary in the initial activation of Raf, so if Raf is ON, Raf will remain ON with or without Ras [7], however, if Ras, Raf, and the negative regulators are ON, Ras will let Raf stay ON [77]. \n\nNote: our Raf is separated into several nodes (see logic tables below) so that more realistic and precise simulation can be conducted. Raf represents the final state of the Raf protein, therefore all the negative and post-activation regulation takes place on Raf. When Raf is deactivated it turns into a resting version of Raf (Raf_rest) [77, 30, 77]. Upon PP2A dephosphorylation of resting Raf is ready (Raf_DeP) [60, 46, 77, 85, 15, 79, 43, 48, 30, 77] to be translocated to the membrane (Raf_loc) by GTP-bound Ras [7, 30, 77]. Localized Raf then has to loose RKIP which sequesters sites in the activation loop of Raf. [31, 87, 49, 69] The last step of Raf activation consists of Src and PAK phosphorylation of the activation site of Raf itself[82, 79, 87].\n\n

*Akt is a negative regulator of Raf {[40]-p(5), Fig. 1, [70]-p(1), [77]-p(5)}\n<br>*Akt phosphorylates Raf at S259 which inhibits activity of Raf and its activation by upstream stimuli {[54]-p(2)}\n<br>*Raf1 is a substrate of Akt {[17]-p(900)}\n<br>*Akt is a potent inhibitor of Raf1 primarily in myoblast and breast cells {[42]-p(4)}\n<br>*Raf1 is an Akt target {[16]-p(195)} \n<br>*Akt suppress Raf-1 activity by phosphorylation of serine-259 {[79]-p(292, 299), Fig. 3, table 1}\n<br>*AKT can phosphorylate C-RAF at S259 {[48]-p(877)}\n<br>*blocking Akt severly impaired Raf-induced transformation. {[38]-p(5)}\n<br>*Akt can phophorylate and deactivate Raf. {[30]-p(217)}\n\n

*Pak activates Raf and Mek {[61]-p(2), Fig. 1, [4]-p(2)}\n<br>*PAK phosphorylates Raf on Ser338 {[74]-p(3), [54]-p(2), [77]-p(6)}; this phosphorylation seems to be required for the integrin activation of Raf {[77]-p(6), [74]}\n<br>*PAK can activate Raf {[25]-p(4)}\n<br>*Raf is a PAK substrate {[71]-p(759)}\n<br>*Pak -3 can phosphorylate raf-1 on serine-338. Pak can activate raf-1 {[79]-p(293), Fig. 3}\n<br>*Pak phosphorylates Raf {[52]-p(1)}\n<br>*Raf1 is a target of PAK {[39]-p(165)}\n<br>*PAK can activate C-RAF which is RAS-independent {[48]-p(876)}\n\n

*RKIP inhibits Raf-1 by not allowing Src and PAK phosphorylation of Raf-1. {[31], [87], [49], [69]}\n<br>*RKIP has to be activated/phosphorylated to leave Raf {[69]}\n

*Ras as an upstream of Raf {[26]-(fig.1,p.2), [89]-p.3, [29]-p.5, [23]-p.161, [10]-p.3,fig.1, [63]-p(2-fig.1), [65]-p(3), [88]-p(1), [85]-p(3), [80]-p(1)}\n<br>*Raf is affected by Ras {[12]-p.7,[24]-p.1, [40]-p.5, [9]-p.2}\n<br>*Ras activates Raf {[32]-p.1, [11]-p.4, [50]-p.1, [86]-p.161, [53]-p.106, [57]-(p.3,fig.2), [47]-(p.41,fig.6), [25]-p.2, [21]-p.1, [42]-p(1), [78]-p(1), [51]-p(5), [22]-p(6), [34]-p(322)}\n<br>*Ras regulates a number of downstream effectors, including Raf1. {[13]-p(7)}\n<br>*Receptor_mediated activation of Raf is Ras-dependent and involves recruitment of the kinase to the plasma membrane {[74]-p.3}\n<br>*GTP-bound Ras activates Raf {[59]-p.2, [72]-p(33), [85]-p(1), [27]-p(357)}\n<br>*GTP-bound Ras activates Raf; Ras recruits Raf to membrane, where it's activated by Ras-independent mechanism {[77]-p(1), [56]-p(5)}\n<br>*Ras binds to Raf causing its association with membrane where it gets activated upon phosphorylation {[33]-p(2), [58]-p(3)}\n<br>*c-Raf-1 undergoes activation after binding to active p21Ras. {[19]-p(1)}\n<br>*Ras bind to and activates Raf. {[14]-p(1)}\n<br>*Ras recruites Raf to the plasma membrane where it is activated by phosphorylation {[64]-p(2), [37]-p(276)}\n<br>*Raf is believed to be activated by binding to GTPRas. {[41]-p(1)}\n<br>*K-Ras activates Raf1 and Rac1 more efficiently than H-Ras {[36]-p(652)}\n<br>*Ras interacts with, and activated Raf, leading to the stimulation of Mek1/Mek2 and Erk1/Erk2. {[83]-p(1)}\n<br>*Raf has a Ras binding domain, indicating it as a Ras effector. {[83]-p(3)}\n<br>*Ras binds directly to the N-terminal regulatory domain of the RAF proteins and activates Raf {[48]-p(875, 876)}\n<br>*Ras activates Raf-1 by recruiting it in a complex with 14-3-3 to the plasma membrane {[62]-p(374)}\n<br>*K-ras is the more potent activator of Raf-1 than H-ras {[62]-p(374)}\n<br>*Activated Ras recruits Raf. {[80]-p(1)}\n<br>*Ras is a direct Ras effector. {[80]-p(2)}\n<br>*Ras activates Raf by attracting it to the membrane and relieving the autoinhibitory conformation of Raf. This opens the 4 activating sites on Raf. {[30]-p.215}\n<br>*Ras keeps Raf in an active conformation {[20]-p.68}\n\n

*One inhibitory mechanism is mediated directly by phosphorylation of Raf by PKA {[75]-p(3), [66]-p(164)}\n<br>*PKA inhibits Ras activation of Raf and Erks {[22]-p(5)}: Probably overrules the activation of Raf by Ras??!!\n<br>*PKA inhibits Raf, but if active simultaneously with PKC then Raf is activated {[76]-p(8), [77]-p(1)}\n<br>*PKA blocks activation of Raf by preventing it to bind to Ras {[42]-p(2), [77]-p(5)}\n<br>*PKA inhibits Raf by phosphorylating Ser43 and Ser621 {[82]-p(57)}; phosphorylation at Ser621 may be required for Raf activation through 14-3-3 {[82]-p(58, 63)}\n<br>*PKA inhibits Raf by phosphorylating Ser43. {[85]-p(1), [79]-p(294), Fig. 3}\n<br>*Expression of Dominant Negative PKA allows Raf to remain responsive to platelet-derived growth factor(PDGF) even in suspended cells. {[90]-p(1)} \n<br>*Phosphorylation of Raf-1 by PKA diminishes its affinity for Ras. This phosphorylation on S43 has an effect after Raf has bound to Ras i.e., when Raf is ON. {[77]-p(4)}\n<br>*In C. elegans, PP2A was identifed as a positive effector of Ras signalling, whereas, in drosophilia, PP2A was found to have both positive and negative effects on the Ras pathway. {[43]-p(5)}\n<br>*All of effects of PKA are mediated through S259 of C-Raf although three sites of C-Raf (S43, $233 and S259) are PKA targets, and inhibits C-RAF. BUT the authors said all of three sites contribute to the inhibition by PKA {[48]-p(877)}\n<br>*PKA can phophorylate and deactivate Raf. {[30]-p(217)}\n\n

S_21 1 S_103 1 S_234 1 S_44 1 S_177 1 S_244 1 S_108 1 S_21 1 S_191 1 S_177 1 S_177 1 S_103 1 S_234 1 S_133 1 S_44 1 S_177 1

EGFR_T669 (Threonine 669 site of EGFR) is phosphorylated (hence activated) by Erk.\n\n

Erk phosphorylates EGFR T669 (which results in decreased kinase activity, internalization, and substrate specificity of EGFR) [1, 2, 4, 3].\n\n

S_234 1

S_213 1 S_22 1

ErbB3_Y1035 (Tyr_1035 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1035 (Tyr_1035 site of ErbB3) is activated upon receptor dimerization [1].\n\n

S_20 1 S_91 1 S_99 1

S_165 1

Clathrin is recruited by [[AP2/Epithelial|AP2]], [[GAK/Epithelial|GAK]], [[ESCRT_0/Epithelial|ESCRT_0]], [[Src]],[[Hip1R/Epithelial|Hip1R]], or ([[PIP2_45]] AND ([[Epsin/Epithelial|Epsin]] OR [[CALM/Epithelial|CALM]])).{[12, 2, 4, 11, 6, 15, 10, 17, 5, 7, 18, 9, 14, 13, 3]} \n\n\n

*Src kinase mediates phosphorylation of clathrin.{[12], p-(540)}\n\n

*Hrs (component of ESCRT_0) recruits clathrin to (late) endosomes whereas, clathrin binding restricts Hrs to microdomains that are required for efficient EGF degradation.{[3]-p(357)}\n

*Increased PIP2_45 is required for Clathrin. {[16]}\n\n

*GAK (auxilin2) promotes the assembly of clathrin into clathrin-coated vesicles.{[4], p-(641)}\n\n

*Hip1R binds to the clathrin coat, possibly stimulating or stabilizaing its assembly and binds to actin filaments.{[15], p-(1199)}\n<br>*Hip1R can bind to both F-actin and to polymerized clathrin at the same time and can promote assembly of clathrin and F-actin into higher order structures.{[1], p-(1199)}\n<br>*Hip1R bridges endocytic vesicles to the actin cytoskeleton by binding binding to clathrin and actin.{[9], p-(4594)}\n<br>*Hip1R binds to clathrin and also associates with AP2.{[13]-p(417, 418)} \n<br>*Hip1R recruits clathrin and AP2 to the plasma membrane.{[7], p-(312)}\n\n

*CALM can bind PIP2_45 and clathrin at the same time and recruit clathrin to the membrane.{[6], p-(1051)}{[2], p-(1363)}{[11], p-(304)}\n<br>*CALM interacts with clathrin and AP-2 and binds to PIP2_45.{[10], p-(2,6)}\n<br>*CALM is capable of recruiting clathrin.{[10], p-(2,6)}\n\n

*AP2 complexes recruit clathrin to the plasma membrane.{[18], p-(95)}{[14], p-(385)}{[2], p-(1362)}{[11], p-(304)}{[5], p-(929)} \n<br>*AP2 binds clathrin and can stimulate clathrin cage assembly.{[6], p-(1051)}{[11], p-(304)}{[10], p-(4)}{[17], p-(507)} \n\n

*Epsins bind to clathrin and phospholipids and promote clathrin assembly.{[11], p-(304)}{[10], p-(3)}\n\n

S_232 1 S_118 1 S_159 1 S_215 1 S_36 1 S_118 1 S_11 1 S_245 1 S_244 1

EGFR_Y1045 (Tyr_1045 site of EGFR) is autophosphorylated (hence activated) upon EGFR activation and dimerization. Hence, this node is activated by the following dimers used in the model: [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] (EGFR homodimer activated by EGF), [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]] (EGFR homodimer activated by TGFa), [[EGFR_EGFR/Epithelial|EGFR_EGFR]] (EGFR homodimer activated by ligand-independent processes; e.g., GPCR_transactivation), [[EGFR_ErbB2/Epithelial|EGFR_ErbB2]] (EGFR_ErbB2 heterodimer), and [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] (EGFR_ErbB3 heterodimer), and [[EGFR_ErbB4/Epithelial|EGFR_ErbB4]] (EGFR_ErbB4 heterodimer).\n\n

*Y1068 and Y1086 are phosphorylated upon EGFR activation [1]\n<br>*Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

Y992, Y1045, Y1068, Y1086, Y1148, and Y1173 are phosphorylated upon receptor dimerization. [1]\n\n

S_214 1 S_99 1 S_157 1 S_195 1 S_52 1 S_194 1

Endophilin is recruited by [[CIN85]] OR [[Eps15/Epithelial|Eps15]] OR [[Epsin/Epithelial|Epsin]].{[1, 2, 3, 4]} . Endophilin can also recruit itself in the presence of PIP2_45.{[1]}\n\n

*Endophilin binding to the phospolipid causes further bending of the membrane. Thus endophilin acts as positive feedback loops on itself by beding and then binding to the newly bent membrane.{[1]-p(494-496)} \n\n\n

*Sensing the curvature of membrane phospholipids caused by epsin, endophilin and amphyiphysin bind to the phospholipid.{[1]-p(494-496)}\n\n

*Eps15 can recruit endophilin.{[3]-p(910)}\n\n

*Endophilin is recruited by CIN85.{[4]-p(183)} \n<br>*CIN85 recruits endophilins to complexes with activated receptors, controlling receptor internalization.{[2]-p(3154)}\n\n

*Epsin can recruit endophilin.{[3]-p(910)} \n\n

S_105 1 S_36 1 S_185 1 S_118 1 S_225 1

ILK is necessary and sufficient to activate B_Parvin. [2, 1]\n\n

*ILK is necessary and sufficient to activate beta-Parvin. {[2]-p(53),[1]-all}\n\n

S_217 1

Activation (creation) of cAMP is through AC [2, 1, 11, 10]. PDE4 is a negative regulator of cAMP, and we are making it dominant based on the strong localization of PDE4 (by B_Arrestin binding) to the site of cAMP production [9, 13, 3]. \n\n

*cAMP is donwstream of AC {[2]-p(1)}\n<br>*Gas activation stimulates AC to elevate intracellular cAMP and activation of PKA {[1]-p(1)}\n<br>*Ac activates cAMP {[11]-Fig. 7}\n<br>*cAMP is produced from AC {[10]-p(1)}\n\n

*PDE4 A-D exlusively hydrolyse cAMP {[7]-p(1952)}\n<br>*The action of PDE4 is the only way to degrade cAMP {[9]-p(1187)}\n<br>*PDE4 is localized to cAMP via Barrestin; thus it is a dominant negative. {[13]-p(130, 131)}\n<br>*b-arrestin 2 recruits PDE4D isoforms into a complex with the activated b2AR, where it's posotioned to degrade cAMP {[3]-p(1)}\n

S_209 1 S_166 1 S_188 1 S_166 1

S_240 1

ErbB3_Y1309 (Tyr_1309 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3]] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1309 (Tyr_1309 site of ErbB3) is activated upon receptor dimerization [1].\n\n

S_91 1 S_99 1 S_20 1

RKIP is 'ON' when it is phosphorylated by PKC. Therefore, PKC is a positive regulator of RKIP. [1, 3, 4, 2]\n\n\n

*PKC phosphorylates RKIP to release its inhibitory effect on Raf. RKIP then switches over to GRK2 and inhibits that. {[1]}\n<br>*PKC is essential for RKIP to be released from Raf and inhibit GPCRs {[4]-p(92)}\n<br>*PKC activates RKIP which makes it leave Raf and look for a new substrate {[2]}.\n<br>*PKC phosphorylation on S153 is required for RKIP activation ond GRK2 inhibition {[2]-p(575)}

S_240 1

Rab5 is involved in the regulation of early endosome functions{[]}, and it is activated by [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]], [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]]{[6]}, Rabex_5{[11, 7, 1, 2]}, RIN{[6, 10]}, P120RasGAP{[8]}, Rabaptin_5-Rabex_5 complex{[2, 1]} OR (EEA1,Rabex_5 AND Rabaptin_5){[]}. Rab5 is inactivated by Rab7.{[6]} This inactivation occurs only when Rab5 was previously ON. Positive regulators are dominant to the negative regulation when Rab5 and Rab7 are active.\n\n

*EGFR activates Rab5 and induces translocation of EEA1 from the cytoplasm to the membrane of early endosomes.{[6]-p(351)} \n\n

*Initially Rab5 activates Rab7 until Rab7 reaches a threshold upon which it inactivates Rab5 through a negative feedback loop.{[6]-p(354)} \n

* \n<br>*Rabex_5 functions as a guanine-exchange factor for Rab5.{[11]-p(1942)}{[7]-p(547)}{[1]-p(3)}\n<br>*Rabaptin_5-Rabex_5 complex activates Rab5 through the nucleotide-exchange activity of Rabex_5 and gets recruited on the early endosome membrane through Rabaptin_5.{[2]-p(111)}. \n<br>*Rabex_5 is a specific GEF for Rab5 and Rab21 [1] \n\n

*RIN activates Rab5 and links the Ras signaling pathway with endocytosis signaling {[10]}\n<br>*RIN promotes EGFR endocytosis through its Rab5-GEF activity{[6]-p(356)}\n\n

S_192 1 S_124 1 S_192 1 S_230 1 S_124 1 S_192 1 S_52 1 S_124 1 S_192 1 S_238 1 S_124 1 S_192 1 S_157 1 S_124 1 S_192 1 S_25 1 S_124 1 S_192 1

GCK is activated by Trafs {[4], <cite>Lewis</cite>, [3], <cite>Lee</cite>}. \n\n

*Trafs can possibly activate GCK, but there is a question. {[4]-p(836)}\n<br>*TNF definitely activates GCK, but whether it is mediated by trafs is not certain. {[4]-p(836)}\n<br>*GCK is stimulated in response to TNF (through Trafs though?) {[2]-p(72), [1]-p(8383)}\n<br>*Recruitment to the membrane by upstream activators such as TRAF2 creates a higher_order aggregate that activates GCK and alters the conformation of the components in the complex, forcing MEKK1 into oligomeric state that fosters its activation. {[3]-p(745)}\n\n

S_123 1

This node represents the homodimer of EGFR activated by other (non-EGF and non-TGFa) signaling components. The current version of the model includes EGFR transactivation by G-protein Coupled Receptors. The activation of EGFR by GPCR is mediated via alpha-q_R, alpha-i_R OR alpha-12_13_R. However, this activation seems to occur only when EGFR_T654 is phosphorylated and Ca present [8, 12, 24, 26]. In addition, EGFR_Free has to be active for EGFR_EGFR to be activated. Note that in the most recent version of the model, until more data on internalization of EGFR activated by GPCR is found, the internalization process of EGFR_EGFR is not being modeled in detail.\n\n

* EGFR monomer is assumed to be necessary for the activation.\n\n

*EGFR is phosphorylated by PKC. This blocks EGFR dimerization, which means EGF can't work. But this block in dimerization means GPCR CAN work (and PKC/CA is required for this transactivation). {[8]-p(2), [12]-p(540)}\n<br>*It has been reported that EGFR transactivation requires Ca and/or PKC {[24]-p(3), [26]-p(1204)}\n<br>*Activation of PKC is required for Gq-coupled receptors to induce EGFR transactivation {[36]-p(2)}\n<br>*PKC is required for Gq to induce EGFR {[36]-p(2)}\n<br>*Gq stimulation of EGFR requires Ca {[36]-p(2)}\n

S_24 1 S_41 1 S_229 1 S_149 1 S_67 1 S_229 1 S_149 1 S_41 1 S_213 1 S_149 1 S_229 1 S_41 1

This node represents the EGFR:ErbB2 heterodimer activated by EGF on the cell surface. It is activated by EGF AND EGFR_Free (representation of an inactive EGFR) AND ErbB2_Free (representation of an inactive ErbB2), unless EGFR_T654 is active. Due to the hierarchy in the activation of the various ErbB's, the activation of EGFR_ErbB2 occurs unless both ErbB3_Free AND NRG are present. Pertuzumab blocks the formation of the dimer (and hence the activation of the complex). Trastuzumab is a negative regulator once the dimer is active. \n\n

See ErbB3_Free above.\n\n

Antibody that negatively regulates ErbB2. The mechanism of this negative regulation seems, however, still unclear and/or contradictory []. But because it appears Trastuzumab doesn't affect the dimerization step, it will be a negative regulator of the dimer once it has been activated. This way, it will also be complementary to the mechanism of Pertuzumab.\n\n

*(Our EGF represents both EGF that is specific to EGFR and EGF_like ligands that result in the activation of the EGFR:ErbB2 homodimer)\n<br>*EGF activates EGFR {[3]-p(3), [13]-p(1), []-p(4-Fig. 2), [10]-p(1), []-p(1), []-p(2-Fig. 1)}\n<br>*EGFR autophosphorylates at five known tyrosine residues after the addition of EGF {[13]-p(2)}\n<br>*EGF is known to activate EGFR {[7]-p(3)} \n<br>*EGF binds EGFR {[1], <cite>Schoeberl</cite>-p(1)}\n<br>*EGF binds to EGFR which causes dimerization and subsequent cross-phospohrylation of specific residues in the C-terminal tail of teh partnering receptor{[1], <cite>Schoeberl</cite>-p(564)}\n\n

EGFR_ErbB2 is activated by EGFR_Free, which represents unliganded EGFR on the cell surface.\n\n

EGFR_ErbB2 is activated by ErbB2_Free, which represents inactive ErbB2 on the cell surface.\n\n

ErbB2:ErbB3 appears to be the most potent heterdimer and is predominant in carcinoma cells [11]. Therefore to capture this hierarchy in the ErbB signaling network, ErbB3_Free (AND NRG) will be a negative regulator to EGFR_ErbB2.\n\n

S_195 1 S_50 1 S_195 1 S_247 1 S_162 1 S_195 1 S_114 1 S_107 1 S_31 1 S_149 1 S_41 1 S_117 1 S_195 1 S_195 1 S_162 1

Very little information is known about the activation of PTEN. Cdc42-alphaPIX complex AND Rho AND PI3K have to be present to activate/recruit PTEN [10, 5]. PTEN can be also activated by stress [3, 2]. Src deactivates PTEN when PTEN is ON [2]. \n\n

*Src kinase phosphorylates PTEN, leading to reduced stability as well as inhibition of its phosphatase activity {[2]-p(12)}\n

*RhoA is activates PTEN through phosphorylation by ROCK and is required for the activation. {[10], [5]}\n\n

*PI3K is required, along with Rho and Cdc42 for the translocation/activation of PTEN {[5]}\n\n

*PTEN is sensitive to cellular redox {[2]-p(6)}\n<br>*PTEN activity is induced upon cell stress through p53 {[3]-p(4, 5)}\n\n

*Cdc42-aPIX and Rho are required for the activation of PTEN {[10], [5]}\n\n

S_86 1 S_82 1 S_40 1 S_228 1 S_219 1 S_132 1 S_82 1

S_213 1 S_197 1 S_89 1 S_197 1 S_89 1 S_242 1

Gab1 activates SHP2 {[10, 3, 6, 4, 12, 9, 13, 2, 8]}.\n\n

*Assosiacion with Gab1 promoted by EGF {[10]-p(5)}\n<br>*SHP2 is recruited/activated by Gab1 {[3]-p(2, 7), Fig. 10, [6]-p(2), [4]-p(4), [12]-p(3)}\n<br>*SHP2 binds to Gab1 through its SH2 domains {[9]-p(4)}\n<br>*SHP2 directly binds to Gab1 {[13]-p(1)} that is tyrosine kinase phosphorylated {[13]-p(6)}\n<br>*Gab1 and Gab2 are associated with SHp2 in a tryosine phosphorylation-dependent fashion and seem to participate in multiple signaling pathways {[2]-p(2)} \n<br>*In response to EGF, Gab1 is recruited by Grb2 in the vicinity of EGFR and becomes phosphorylated. This causes the activation of SHP2 and PI3K {[8]-p(5350)}\n

S_154 1

Src is a positive regulator of p190RhoGAP [1, 2, 17, 3, 11, 13, 14, 5, 6]. p120RasGAP is a negative regulator [16], it turns p190RhoGap OFF when it is ON. p120RasGAP will be dominant since there is no information on which is dominant and making p120RasGAP dominant means it will not drop out of the logic. However, this negative regulation can be overcome by Fak AND Src that allow Paxillin to bind p120RasGap, therefore displace p190RhoGap.[15]\n\n

*p190GAP is regulated by Src {[1]-p(7), [2]-p(5), [17]-p(7)}\n<br>*Active v-Src is required for tyrosine phosphorylation of p190RhoGAP and binding to p120GAP {[3]-p(25)}\n<br>*possibility that p190RhoGap phosphorylation by Src following EGFR activation activates activity of p190 {[11]-p(562)}\n<br>*Activation of Src leads to phosphorylation of p190, which recruits p120 RasGAP. This effectively activates p190RhoGAP. {[2]-p(7)}\n<br>*Src phosphorylates p190RhoGAP {[13]-p(12), [14]-p(125), [5]-p(7938), [6]-p(276)}\n\n

S_135 1 S_244 1 S_244 1 S_199 1 S_238 1 S_135 1

Talin is required for (inside-out) activation of Integrins [42, 7, 31, 8, 17, 45, 20, 25, 28]. ECM is required for (outside-in) activation [16, 30, 29, 19, 10, 4, 43, 14, 6, 21, 40]. When Talin AND ECM are ON, Integrins are activated and clustered. That will define Integrins as ON for the model.\nSrc deactivates Integrins by direct phosphorylation of Integrins that displaces Talin [34, 31, 46, 19, 44, 22, 24]. Src deactivation is dominant to Talin activation, but only when Integrins are ON [17].\nILK also phosphorylates Integrins [36, 12] and it is likely that that phosphorylation negatively regulates Integrins [36, 9, 23, 3], although there is some dispute [33]. In the model ILK phosphorylation of Integrins will negatively regulate it by displacing Talin.\nPP2A dephosphorylates the Integrin tail [35, 17, 3], it will be dominant to ILK when Integrins are OFF, allowing ECM AND Talin to activate. Thus, when ILK is ON and Integrins are OFF, a combination of PP2A AND ECM AND Talin will turn Integrins ON.\n\n

*Src family kinases reduce integrin b tails by phosphorylation of the BPxY motifs on integrins. It may be an important negative regulator of integrin activation {[34]-p(5),[31]-p(3)}\n<br>*b-integrin is a potential substrate of Src {[46]-p(9)}\n<br>*v-Src can phosphorylate Integrins {[19]-p.529}\n<br>*v-Src can directly phosphorylate b-intergin subunits and suppress their activity {[44]-p(124)}\n<br>*vSrc induces tyrosine phosphorylation of B1A integrin subunits {[22]-p(3)}\n<br>*c-Src can be directly activated by binding and clustering of particular b-integrin cytoplasmic tails such as b3-integrins. {[24]-p(2)}\n<br>*Src phosphorylates beta tails of integrins which displaces talin, however this is only after they have been activated. Initial activation can't be regulated by tyrosine phosphorylation {[17]-p(431)}\n<br>*Src phosphorylation of integrin tails leads to reduced talin binding. {[28]-p(28894)}\n\n

*Interaction of the b subunit with Talin is important for integrin activation {[42]-p(9)}\n<br>*the N-terminal head domain of talin can activate integrins by binding directly to the integrin b1 or b3 cytoplasmic domains. And talin is the major integrin-proxiaml effector of inside-out integrin activation. {[7]-p(95)}\n<br>*Talin activates integrins {[31]-all}\n<br>*Binding of Talin to integrins is increased by PIP2_45 {[2]-p(2325)}\n<br>*Talin is required for inside-out integrin activation {[8]-p(55)} and might be even required for the signaling through ECM {[8]-p(55)}\n<br>*Talin is required for Integrin activation. {[31]-p.435, [17]-p(431)}\n<br>*Integrin signalling via FAK and Src promotes binding if talin to a PIP kinase. Complex formation activates a PIP kinase and protmotes translocation of talin to the plasma membrane, although the latter is independent of kinase activity. Talin is activated in the membrane by the localized production of PIP2_45, exposing the integrin-binding site. Talin might then activate integrins and also provide a link to the actin cytoskeleton {[45]-p(832)}\n<br>*Integrins don't bind Talin in unstimulated cells {[20]-p(133)}\n<br>*Talin binding to integrin beta tail activates integrins, and disruption of the integrin-talin interaction prevents integrin activation. {[28]-p(28889)}\n<br>*Talin binding to integrins is the final and necessary step in their activation. {[25]-all, [28]-p(28889)}\n<br>*"Talin links integrins to the actin cytoskeleton and may contribute to integrin clustering" {[27]-p(695)}\n\n

*Integrins are regulated by ECM {[16]-p.1/2,[30]-p.2,[29]-p(6361)}\n<br>*Integrins mediate cell-matrix and cell-cell interactions {[19]-p.529,[10]-p.1,[15]-p(1)}\n<br>*ECM faciliate integrin activation {[4]-p(234)}\n<br>*Integrins bind to ECM {[43]-p(1)}\n<br>*integrins relay signals from ECM {[14]-p(767)}\n<br>*Because integrin ligands are multi-valent, integrin clustering can activate integrins (increase avidity). This is outside-in signalling. {[6]-p.E65}\n<br>*Clustering of integrins is usually thought of as being induced by ECM. {[21]-p.412,[40]-p.4234}\n\n

*ILK is probably capable of inside-out regulation of integrins. -> could be only in epithelial cells,though {[30]-p.11}\n<br>*Upon stimulation by PIP3_345, ILK catalyzes serine/threonine phosphorylation of integrins {[5]-p(2)}-although it's not known if it works in vivo\n<br>*ILK phosphorylates serine/threonine res. on beta1-peptides {[36]-p(93)}\n<br>*Knockdown of ILK by RNA interference inhibits phosphorylation of Thr788-789 of b1 integrin cytoplasmic domain {[12]-p(53,fig.2)}\n<br>*B1 cytoplasmic domain is an ILK substrate {[12]-p(55,table1)}\n<br>*ILK phosphorylates integrin beta tail, most likely on Thr788-789. {[12]-p.53,55} There are two papers that indicate that phosphorylation of Thr788-789 negatively regulates integrins [23]-all, [9]-all, one that shows that the lack of Ser/Thr phosphatase activity blocks beta-1 actin binding [3], and one that shows that overexpression of ILK inhibits integrin activity. {[36]-all} This is all evidence that ILK phosphorylation of integrins negatively regulates integrins (probably through the displacement of talin {[31]-p.436}. There is one paper that says phosphorylation of integrins on Thr788-789 is required for integrin activity. {[33]-all} Since this paper is in the minority, we will not use it.\n\n

*PP2A plays a role in integrin inside-out signaling.PP2A colocalizes with b1 integrin. Inhibition of PP2A induces selective loss of b1 integrins. {[35]-p(1)}\n<br>*At the integrin level, v-Src has been shown to influence integrin function by direct phosphorylation of tyrosine residues {[38]-p(7941)}\n<br>*PP2A dephosphorylates integrins, and is necessary for integrin activation. {[3]-all}\n

S_218 1 S_23 1 S_200 1 S_217 1 S_43 1 S_200 1 S_218 1 S_217 1 S_23 1 S_244 1 S_218 1 S_200 1 S_217 1 S_23 1 S_43 1 S_200 1 S_244 1 S_217 1

The main activator of Gai is the GPCR alpha-i_R {[17, 1, 3, 12, 11]}, but alpha-s_R can also stimulate [5, 1, 11]. Gbg_is a GDI for Gai, which keeps Gai OFF when it is OFF {[7, 9, 8, 12]}. PKA is a positive regulator {[5, 1, 13, 15]}.\nGai is activated by alpha-i_R when Gai is OFF AND Gbg_is OFF {[1, 7, 9, 8, 5, 1, 11]}. Alternatively, Gai is activated when Gai is OFF AND alpha-s_R is OFF AND PKA is ON and alpha-s_lig are ON {[5, 1, 11, 13, 15]}.\nRGS is a negative regulator {[10, 6, 2, 14, 18, 12]}. Also, Gai is deactivated by RGS when Gai is GTP-bound (i.e., ON) {[10, 6, 2, 4, 12]}. We are requiring RGS to stimulate the GTPase activity of Gai, so if Gai is ON and RGS is OFF, Gai will stay on even in the absence of alpha-i_R OR alpha-s_R activation when Gbg_i is ON (otherwise, RGS would simply drop out of the logic).\n\n

*RGS functions as a GAP toward Ga subunits but not Gbg {[10]-p(1), [6]-p(2)}\n<br>*RGS binds to Gai to stop its activity {[2]-p(529)}\n<br>*RGS is a GAP for Ga {[14]-p(1), [18]-p(1301)}\n<br>*Many RGS proteins catalyze reapid GTP hydrolysis by isolated Ga subunits in vitro and attenuate agonist/GPCR_stimulated cellular responses in vivo {[12]-p(555)}\n\n

*PKA and PKC have been shown to desentitize GPCR in a feedback regulatory fashion. {[5]-p(2), [13]-p(1189)}\n<br>*PKC and PKA phosphorylate GPCR and substantially impair its ability of purified receptors to stimulate their G-prot. {[1]-p(655)}\n<br>*PKA has to be present in order for GPCR to bind Gai {[5]-p(18679)}\n<br>*PKA pshophorylates GPCR after it has been desentizised by GRK and b-arrestin. Note, that the receptor is inactive because of the sequestering, but not due to lack of stimuli. [15] (Therefore, the activator needs to be present in the logic of Gai)\n\n

S_67 1 S_222 1 S_201 1 S_133 1 S_222 1 S_55 1 S_187 1 S_201 1 S_222 1 S_201 1 S_156 1

S_247 1 S_220 1 S_195 1 S_91 1

MLK3 is activated by Rac and Cdc42 [5, 4, 3, 2] or the IL1-TNFR [6]. \n\n

*MLK2 and MLK3 interact with Rac-GTP and CDC42-GTP through their CRIB motif {[3]-p(70)}\n<br>*MLK3 is activated by Rac and/or Cdc42 {[2]-p(666}\n\n

*The TNFR can activate MLK3. {[6]-all}\n

*MLK3 is a downstream effector of Cdc42 {[5]-p(1), [4]-p(828)}\n<br>*MLK2 and MLK3 interact with Rac-GTP and CDC42-GTP through their CRIB motif {[3]-p(70)}\n<br>*MLK3 is activated by Rac and/or Cdc42 {[2]-p(666)}\n\n

S_132 1 S_160 1 S_61 1

PIP2_45 [2, 8, 4, 9, 5, 7], AA [2], or PKC [6] are all negative regulators of RhoGDI. They are in an OR relationship. \n\n

*PIP2_45 is a negative regulator of RhoGDI. It works by activiating ERM's (not in the network) which then sequesters RhoGDI, blocking its activities. {[8]-p(3687), [2]-p(26209), [4]-p(643), [9]-all}\n<br>*PIP2_45 may be able to displace RhoGDI on its own. {[5]-p(768)}\n<br>*Phosphoinositides at least partially dissociate RhoGDI from Rho. {[7]-all}\n\n

*PKC phosphorylation of RhoGDI causes it to dissociate with Rac. {[6]-all}\n

S_240 1 S_118 1 S_182 1 S_118 1 S_240 1 S_182 1

ErbB3_Y1203_05 (Tyr_1203/05 site of ErbB3) is activated when ErbB3 dimerizes with [[EGFR_ErbB3/Epithelial|EGFR_ErbB3]] OR [[ErbB2_ErbB3/Epithelial|ErbB2_ErbB3] OR [[ErbB3_ErbB4/Epithelial|ErbB3_ErbB4]].\n\n

ErbB3_Y1203_05 (Tyr_1203/05 site of ErbB3) is activated upon receptor dimerization [].\n\n

ErbB3_Y1203_05 (Tyr_1203_05 site of ErbB3) is activated upon receptor dimerization [].\n\n

S_20 1 S_99 1 S_91 1

UBPY is recruited by STAM (a component of ESCRT_0), ESCRT_III or Alix.{[1, 4, 3, 5, 2]} \n\n

*Alix mediates the recruitment of the Ub hydrolase degradation of AMSH, UBPY that deubiquitylates MBV cargoes. {[3]-p(645)}\n<br>*UBPY is recruited by Alix.{[5]-p(449)}\n\n

*UBPY is recruited by ESCRT_III. {[5]-p(449)}\n

S_102 1 S_15 1 S_122 1

Rho stimulates PI4K [2, 5], as does PKC [3], Gai [3], Gaq [3], and ARF [4]. All of these are in an OR relation. \n\n

*PI4K is downstream of Rho {[2]-p(6), Fig. 9}\n<br>*PI4k activated by RhoA {[5]-p(16913)}\n\n\n

*PKC can activate PI4K {[3]-p(284)}\n\n

*Arf activates PI4K by recruiting it to the membrane {[4]-p(514)}\n

S_240 1 S_12 1 S_201 1 S_7 1 S_228 1

AC in the model is based on AC 4 and AC 7 because of their wide-spread distribution. Gas stimulates AC [18, 7, 3, 20, 12, 4, 13], Gai does not inhibit AC 4 or 7 [13, 16] so it is not included as an input. Gbg_i stimulates AC 4 and 7 [13, 19], but only in conjunction with GTP-bound Gas [19, 12, 8]. We are defining AC as ON at the activity level achieved when both Gas and Gbg are ON, so they are in an AND.\nPKC can stimulate AC 4 or 7, but it does not appear to be necessary for AC 4 or 7 activation [13, 16] so it is included as an input but it drops out of the logic. \nMoreover, cAMP/PKA pathway is regulated by integrin-mediated adhesion to te ECM, however, a clear mechanism to do so doesn't seem to have been suggested [1], therefore, we will have Integrins AND ECM as a condition to activate AC. This connection, however, will be revisited as soon as a clear mechanism is found. \n\n

*AC is downstream of Gas(positive),Gbg(positive-not in network) and Gai(negative) {[18]-p5(460)}\n<br>*AC-cAMP pathway is activated by Gas {[7]-p.1,[10]-p(1)}\n<br>*Gas activation stimulates AC to elevate intracellular cAMP and activation of PKA {[3]-p.1}\n<br>*AC is activated by Gas. {[20]-p(2), [13]-p(1940)}\n<br>*Gas selectively inhibits AC types V and VI. {[20]-p(2)}\n<br>*Type II AC is activated by Gbg when Gas is bound. {[20]-p(2)}\n<br>*Gas activates AC {[12]-p(670), [4]-p(3), [15]-p.554}\n\n

S_200 1 S_23 1 S_222 1 S_241 1

Uncoating of clathrin is mediated by Hsc70 and auxilin.{[1]} Hsc70 is recruited by [[GAK/Epithelial|GAK]] or [[Dynamin/Epithelial|Dynamin]].{[4, 1, 5, 3, 6])} \n\n

*GAK (Auxilin2) recruits Hsc70 to clathrin-coated vesicles to disassemble the clathrin coat.{[4]-p(305)}\n<br>*Auxilin binds assembled clathrin and recruits Hsc70 and stimulates its ATPase activity, which leads to release of the clathrin coat. Hsc70 remains bound to disassembled clathrin and may prime reassembly of clathrin, while auxilin is recycled and promotes multiple rounds of uncoating {[1]-p(R50)}\n<br>*Upon separation from the plasma membrane, endocytic vesicles undergo uncoating in a process mediated by auxilin and Hsc70.{[5]-p(31.8)}{[2]-p(641)}{[3]-p(351)}\n\n

*Dynamin recruits Hsc70 and auxilin.{[6]-p(930)}

S_11 1 S_10 1

This node represents the homodimer of EGFR activated by EGF undergoing slow recycling. Since [[AMSH/Epithelial|AMSH]] promotes slow recycling of the receptor, EGFR_EGFR_EGF_SR is activated when AMSH AND EGFR_EGFR_EGF_MVB are ON {[6]-p(555)}. However, because in our model, we do not have negative regulators of AMSH, the ligand-bound receptor would never degrade in lysosome, which is known to occur (receptor downregulation). Therefore, until more regulators of AMSH are added, the logic table of this node is created not to never turn the node on.\n\n

*Endocytosed EGFR, which can be recycled from the limiting membrane of MVBs, is recycled in active form. []\n\n

*AMSH can deubiquitinate EGFR, and thus it's been suggested that AMSH promotes (slow) recycling of the receptor.{[6]-p(555)}\n

S_16 1 S_47 1

S_130 1 S_177 1 S_212 1 S_212 1 S_130 1 S_130 1 S_177 1 S_212 1

alpha-12_13_R is stimulated by its ligand alpha-12_13. GRK phosphorylates alpha-12_13_R, but this has no effect on its own [13, 4, 5, 6, 12]. When GRK does phosphorylate alpha-12_13_R and B_Arrestin is on, alpha-12_13_R is off [9, 1]. GRK only phosphorylates alpha-12_13_R when alpha-12_13_R is ON [4], so alpha-12_13_R will be an input to itself.\nThe external inputs will not be dominant to the negative regulators (otherwise the negative regulators really have no effect). \nNote, our GPCRs are separated into two nodes so that more realistic and precise simulation can be conducted. Since the phosphorylation of GPCRs and the sequestering by B_Arrestin are two separate events, we have a phosphorylated version of each GPCR. This phosphorylated GPCR (Palpha-q_R,Palpha-12_13_R, etc.) has its own logic table and acts as a node on its own during the simulations.\n\n

*B-arrestin down-regulates GPCR by interrupting the interaction between the receptor and the G-protein. {[9]-p(1534), [5]-all}\n<br>*Membrane recycling can turn off GPRC {[9]-p(1534)}\n<br>*b-arrestins desensitizes 7MSRs by structurally blocking their interaction with G-protein. {[1]-p(1), [5]-all}\n<br>*b-arrestins uncouple the receptor from the G prot. and may target many GPCRs for internalization in specialized membrane areas {[10]-p(1940)}\n\n

S_213 1 S_95 1 S_109 1 S_179 1 S_213 1 S_179 1 S_179 1 S_95 1 S_95 1 S_109 1 S_179 1 S_213 1 S_179 1 S_109 1 S_95 1 S_109 1 S_179 1 S_213 1 S_179 1

This node represents the EGFR:ErbB4 heterodimer. It is activated by EGF AND EGFR_Free (representation of an inactive EGFR) AND ErbB4_Free (representation of an inactive ErbB4) AND NRG, unless EGFR_T654 is active. Due to the hierarchy in the activation of the various ErbB's, the activation of EGFR_ErbB4 occurs only when ErbB2_Free and Erb3-Free are not present.\n\n

*Neurogulins promote ErbB1:ErbB4 heterdimers [] \n\n

*(Our EGF represents both EGF that is specific to EGFR and EGF_like ligands that result in the activation of the EGFR:ErbB4 homodimer)\n<br>*EGF activates EGFR {[4]-p(3), [14]-p(1), []-p(4-Fig. 2), [11]-p(1), []-p(1), []-p(2-Fig. 1)}\n<br>*EGFR autophosphorylates at five known tyrosine residues after the addition of EGF {[14]-p(2)}\n<br>*EGF is known to activate EGFR {[8]-p(3)} \n<br>*EGF binds EGFR {[1], <cite>Schoeberl</cite>-p(1)}\n<br>*EGF binds to EGFR which causes dimerization and subsequent cross-phospohrylation of specific residues in the C-terminal tail of teh partnering receptor{[1], <cite>Schoeberl</cite>-p(564)}\n\n

PKC phosphorylates EGFR at Threonine 654. The exact mechanisms of the effects associated with the phosphorylation of EGFR at T654 is still unclear. Thus far, at least two mechanisms have been proposed.\nIn the first one, the phosphorylation of T654 prevents the dimarization and activation of EGFR, hence reducing the receptor's potential for downstream signaling [8, 9, 5]. \nIn contrast, the second mechanism implicates PKC phosphorylation of EGFR as a switch that redirects EGF_activated EGFR from the lysosome-mediated degredation pathway to the recycling pathway instead [13].\n

EGFR_ErbB4 is activated by EGFR_Free, which represents unliganded EGFR on the cell surface.\n\n

*ErbB2 is the preferred dimerizing partner for all ErbBs []; Hence ErbB2_Free will be a negative regulator of other dimers.\n\n

EGFR_ErbB4 is activated by ErbB4_Free, which represents inactive ErbB3 on the cell surface.\n\n

*EGFR and ErbB4 are more likely to dimerize with ErbB3 (when NRG is present). []; Hence ErbB3_Free will be a negative regulator.\n\n

S_114 1 S_31 1 S_41 1 S_117 1 S_125 1 S_149 1 S_107 1

ESCRT_0 is recruited to endosomes through in part interaction between the FYVE domain of Hrs and the lipid phosphatidylinositol 3-phosphate.\n\n

*Hrs-STAM(ESCRT_0) is recruited by binding of Hrs to PIP3.{[3]-p(644)} \n<br>*Hrs is targeted to the endosomes via its FYVE domain, which binds to the endosomal lipid phosphatidyliositol 3-phosphate.{[5]-p(1)} \n<br>*ESCRT_0 is recruited to endosomes through interaction with PIP3_345.{[4]-p(553)}\n\n

* \n<br>*ESCRT_0 is recruited to the endosomal membrane. {[]-p(611), []-p(351)} Hence, once EGFR is in End, it will initiate the recruiting process.\n

S_227 1 S_74 1

The regulation of Mekk2 is not clear. Mekk2 is associated with Lad in resting cells and Mekk2 must be associated with Lad to be activated. After activation, it is dissociated from Lad, but that dissociation is mediated by the activator, e.g., EGFR [2]. This appears to indicate that activation of Mekk2 by phosphorylation precludes subsequent activation by kinases. Thus, we will say that after Mekk2 is turned ON, it must then turn OFF on the next iteration. At that point Mekk2 can be activated again.\nPhosphorylation of Lad and Mekk2 by EGFR is necessary for the binding of effectors such as Src [6, 2], PI3K [2, 5], Grb2 [2], or PLCg [2]. Thus, EGFR will be in an AND with those inputs. Because our model also accounts for EGFR dimers, EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4 will be all independent activators. Furthermore, because EGFR signaling continues while EGFR is being internalized [3], the following localizations of EGFR will also be regulators of Mekk2: EGFR_EGFR, EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End.\nLad drops out of the logic and is not included as an input. Mip1 is a promising regulator [4], but its mechanism of regulation is not known so it is also not included.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Possible activation by PI3-K, but there is a question {[5]-p(828)}\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Src phosphorylates and activates MEKK2 {[1]-p(1)}\n<br>*Src activates Mekk2 (through Lad?) {[6]-p(661)} \n\n

*see EGFR_EGFR_EGF_PM above.\n\n

Grb2 is a Mekk2 effector [2]\n\n

*Phosphorylation of Mekk2 by EGFR is necessary for the binding of effectors such as Src [6, 2], PI3K [2, 5], Grb2 [2], or PLCg [2].\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_19 1 S_16 1 S_214 1 S_157 1 S_52 1 S_174 1 S_195 1 S_99 1 S_30 1 S_66 1 S_29 1 S_139 1 S_227 1 S_216 1 S_175 1 S_16 1 S_214 1 S_157 1 S_52 1 S_174 1 S_195 1 S_99 1 S_30 1 S_66 1 S_29 1 S_139 1 S_227 1 S_216 1 S_219 1 S_16 1 S_214 1 S_157 1 S_52 1 S_174 1 S_195 1 S_99 1 S_30 1 S_66 1 S_29 1 S_139 1 S_227 1 S_216 1 S_244 1 S_16 1 S_214 1 S_157 1 S_52 1 S_174 1 S_195 1 S_99 1 S_30 1 S_66 1 S_29 1 S_139 1 S_227 1 S_216 1

ILK activation requires PIP3_345 [12, 2, 4, 13, 6]. It also requires phosphorylation on ser343, but the kinase for that is unknown so that requirement will need to be omitted [6].\nWith PIP3_345 activation, ILK is ON and can signal to AKT and GSK3 [6]. However, Integrins need to be ON for ILK to signal to alpha and beta Parvin and participate in focal adhesions dynamics [8, 1, 5, 11, 9, 7]. Thus, integrin stimulation of ILK amounts to a second ON state. Since each node can only have one ON state, integrins will be an input (in an AND relation with ILK) to the Parvins to indicate the two forms of ILK function.\n\n

*The activity of ILK can be stimulated rapidly, but transiently, by cell-fibronectin interactions and by insulin in a PI3K dependent manner, probably mediated via binding of PIP3_345 to a PH-like domain of ILK {[12]-p(7)}\n<br>*PIP3_345 binds ILK through its PH domain {[2]-p(2), [4]-p(8)}\n<br>*PIP3_345 directly regulates ILK {[13]-p(2908)}\n<br>*PIP3_345 binds ILK through its PH domain and activates it {[6]-p(3)}\n

S_74 1

We are defining Talin as ON when it is able to bind Integrins [11, 12]. That means that if Talin was OFF, PIP2_45 is necessary and sufficient to turn it ON. If Talin was ON, and Src OFF, it implies that Talin is bound to Integrins which is sufficient for Talin to stay ON [5, 7, 16, 17, 1, 26, 15, 6, 29, 21, 26, 18, 19, 20]. Even though PIP2_45 can stabilize Talin binding to Integrins, it is not necessary for Talin to remain ON as we're defining it [1, 29]. Src needs to be OFF for Talin to remain ON because phosphorylation of Integrins by Src displaces Talin [, 26, 8, 10, 23, 13, 16, 17, 19]. This negative regulation by Src only occurs when Talin is ON (i.e., bound to Integrins) [8].\nPKC is an input, but it drops out logically because, even though PKC does phosphorylate Talin, the literature is not clear on the effect of that phosphorylation. Some papers say it breaks up cytoskeletal structures [24, 3], others say it does not [28, 2]. \n\n

*Talin is a potential substrate of Src {[27]-p(9), [10]-p(529), [11]-p(108), [23]-p(125)}, but not only potential; not shown. \n<br>*Src family kinase may also phosphorylate talin, but the effects of these modifications remain unclear {[17]-p(5)}\n<br>*Src phos. of talin comes from expressing v-Src. Not clear if this is direct, so will leave out as an input via direct phosphorylation of talin.\n<br>*Src phosphorylation of integrins displaces talin, and this is dependent on whether talin is bound to integrins (see Integrins). {[8]-p(431), [10]-p(529), [23]-p(124), [13]-p(3), [17]-p(5), [16]-p(3)}\n\n

*PIP2 conformationally modulates talin {[5]-p(97), Fig. 1} \n<br>*Talin's interaction with PIP2_45 promotes its binding to the cytoplasmic domain of b1 integrin subunit {[7]-p(577)}\n<br>*PIP2_45 binds to Talin to induce its association with integrin b1 tails. Notably, Talin binds to and activates one splice variant of the PIP2_45-producing enzyme - PIPKIj-90. Therefore, talin can stimulate PIP2_45 production that in turn enhances talin-integrin interactions. {[16]-p(6)} \n<br>*Talin binds to and activates PIP2 producer PIPKIg-90. In turn, PIP2 enhances talin-integrin interactions. However PIPKI90 competes with integrin b tails for the sites of talin. {[7]-p(3)}\n<br>*Talin binds to PIP2_45, which can strengthen teh interaction between talin and integrins {[1]-p(2324, 2325), Fig. 2, [29]-p(89)} \n<br>*PIP2_45 has been shown to activate the integrin-binding site in talin {[26]-p(831), [15]-p(695)}\n<br>*PIPKIg is recruited to FA through binding to talin. This binding increases the activity of PIPKIg, resulting in production of more PIP2_45, which then regulates talin, vinc, and other FA proteins. {[15]-p(697), [6]-p(88)}\n<br>*PIP2_45 is responsible for talin assembly into focal adhesions {[29]-p(91)}\n<br>*PIP2_45 might activate the integrin-binding sites in talin {[21]-p(31208)}\n<br>*Because talin is reported to contain a second integrin-binding site in the rod region nad is also an antoparallel dimer, it is possible that both PIP kinase and integrins may co-exist within talin complexes, and indeed PIP kinase type Ig co-localizes with talin in FA {[21]-p(31208)}\n<br>*This PIP5K targets talin to FA's and is necessary to activate inactive talin. {[26]-p(834), [18]-all} (through PIP2_45)\n<br>*PIP2 is necessary to retain talin in focal adhesions and may additionally be required for FAK activation. {[]-p(92)}\n<br>*Talin requires PIP2_45 for activity {[20]-p(83)}\n\n

S_218 1 S_244 1 S_118 1 S_218 1

PI3K is considered ON when it is recruited to the proximity of its substrates. The following are PI3K regulators.\nRas can activate PI3K [10, 13, 9, 86, 11, 93, 30, 84, 64, 50, 25, 22, 73, 70, 44, 32, 76, 15, 36, 88, 74, 83, 3, 66, 79, 49].\nPhosphorylated tyrosine sites on ErbB3 (Y1035, Y1178, Y1203/05, Y1241, Y1257, Y1270) and ErbB4 (Y1056) also activate PI3K [23]. Src-phosphorylated Y845 and Y920 sites on EGFR also (possibly) provide a binding site for PI3K [67, 56]. Src AND Cbl_FA can activate PI3K [18] E-cadherin can activate PI3K [60].\nGbg_i can activate PI3K [48, 14, 31, 25, 8, 58, 44, 78].\nFak can activate PI3K [63, 4, 6, 22, 80, 61, 33, 40].\nCrk can activate PI3K [1, 26].\nGab1 [43, 5, 35, 16, 59, 82, 76, 85, 62] can activate PI3K.\nRab1 may affect PI3K, but it's not clear [47, 69, 7], so we are leaving it out. \n\n

*p85 subunit of PI3K binds to Y1035, Y1178, Y1203/05, Y1241, Y1257, Y1270 on ErbB3, and Y1056 on ErbB4. [23]\n\n

*PI3K is affected by Ras {[10]-p(7), [13]-p(10), [9]-p(2), [86]-p(2)}\n<br>*Ras is able to regulate PI3K {[11]-p(3)}\n<br>*PI3K is activated by Ras {[93]-p(2), [30]-p(161), [84]-p(162), [64]-p(3-Fig. 2), [50]-p(41-Fig. 6), [25]-p(1), [22]-p(458-Fig. 6), [73]-p(733), [77]-Fig. 3, [44]-p(10), [32]-p(357), [76]-p(1)}\n<br>*PI3K is a target of Ras {[15]-p(1)}\n<br>*Activity of PI3K is increased by GTP-bound Ras {[36]-p(488)}\n<br>*PI3k can be activated by direct interaction with the Ras proto-oncogene {[88]-p(2905, 2906)}\n<br>*Ras is a necessary upstream regulator of PI3k {[74]-p(771)}\n<br>*All class I PI3Ks bind to Ras {[83]-p(2)}\n<br>*Ras binds and activates the p110 of PI3k {[3]-p(212), [66]-p(374)}\n<br>*PI3K has a Ras binding domain, indicating it is a Ras effector. {[79]-p(3)}\n<br>*PI3K is the second best-characterized Ras effector. {[79]-p(5)}\n<br>*Ras bind to and activates PI3K. {[49]-p(1), [32]-p(357)}\n<br>*H-ras is the more potent activator of PI3k than K-ras {[66]-p(374)}\n<br>*PI3K is a downstream target of Ras. {[76]-p(1)}\n<br>*PI3K associates with activated Ras, leading to PI3K activation. {[76]-p(3)}\n<br>*PI3K can be activated in independently of Ras. {[76]-p(3)}\n<br>*H-Ras preferentially stimulates Ras. {[76]-p(3)} \n<br>*Catalytic subunits of PI3K directly interact with GTP-bound Ras. {[76]-p(1)}\n<br>*Ras binds directly to PI3K's 110 subunit and is upstream of PI3K {[81]-p(65)}\n\n

*p85 subunit of PI3K binds to Y1035, Y1178, Y1203/05, Y1241, Y1257, Y1270 on ErbB3, and Y1056 on ErbB4. [23]\n\n

*PI3K is one of the targets of Src {[27]-p(2-Fig. 1)}\n<br>*PI3K is bound to Src {[55]-p.17(137)}\n<br>*PI3K has been shown to interact with Src {[14]-p(517, 518)}\n<br>*PI3K is activated by Src,RPTKs,GPCR and other receptors {[14]-p(567)}\n<br>*PI3K is a potential substrate of Src {[87]-p(9)}\n<br>*Src can up-regulate PI3K activity {[39]-p(2)}\n\n

*PI3K activation by EGFR is mediated by Gab1. {[35]-p(1455)}\n<br>*EGFR + Gab-1 is nec for GPCR to stimulate PI3K {[85]-p(3), [62]-all}\n<br>*Gab1 as a candidate for mediating the activation of PI3K {[43]-p(5)}\n<br>*Interaction of GAB and EGFR activates PI3K {[38]-p(1)}\n<br>*Gab1 can couple the EGFR directly to activation of the PI3K pathway. {[35]-p(1455)}\n<br>*EGFR + Gab-1 is nec for GPCR to stimulate PI3K {[85]-p(3)}\n<br>*When Gab1 is dephosphorylated by Shp2 it negatively inhibits PI3K-Akt pathway {[5]-p(5)}\n<br>*Gab proteins recruit PI3K, which is another route to activate PI3K downstream of EGFR {[5]-p(5)}\n<br>*Gab1 recruits PI3K {[35]-p(1488)}\n<br>*P85 unit of PI3K binds to Gab, activating PI3K {[16]-p(4)}\n<br>*Gab1 upon tyrosine phosphorylation recruits and activates PI3K {[59]-p(1)}\n<br>*Gab1 serves as a docking site for P85 subunit of PI3K {[82]-p(2), [35]-p(1455)}\n<br>*PI3K activation is required for signaling through Gab1. {[35]-p(1451)}\n<br>*Gab1 binds to PI3K and mediates PI3K activation in response to EGF. {[35]-p(1451)}\n<br>*PI3K is an upstream activator and a downstream effector of Gab1. {[35]-p(1455)}\n<br>*Gab1 is a downstream target of PI3K {[76]-p(4)}\n<br>*In response to EGF, Gab1 is recruited by Grb2 in the vicinity of EGFR and becomes phosphorylated. This causes the activation of SHP2 and PI3K {[75]-p(5360)}\n\n

* \n<br>*EGFR/Her_1 doesn't posses a binding site for PI3K. The activation of PI3K by EGFR has been found to be indirect through other signaling components. However, some data suggest that the phosphorylation of Tyr_845 by Src provides a direct biding site for PI3K [67]. Therefore, EGFR_Y845 is an upstream node of PI3K.\n\n

*PI3K binds to FAK {[63]-p(5-Fig. 3, 12), [4]-p(1), [6]-p(4), [22]-p(442), Fig. 3}\n<br>*PI3K is activated by FAK either directly or through the Src kinase {[80]-p(1)}\n<br>*PI3K binds directly to FAK, which causes the activation of PI3K by FAK {[61]-p(64-Fig. 5)}\n<br>*PI3K binds to Y397 of Fak (after Y397 is phosphorylated). {[33]-p(1411), [40]-all}\n<br>*FAK binds and activates PI3k {[3]-p(212)}\n<br>*Fak contains tyrosines that upon phosphorylation can bind to the SH2 domains of several molecules including Src kinases, PTEN, Grb2, Grb7, nad PI3K, and proline-rich domains that can bind to Cas, Graf, PLCg {[51]-p(3584)}\n\n

*PI3K can bind to the SH3 domain of Crk {[1]-p(234)}\n<br>*viral oncoprotein v-Crk was shown to activate PI3K, which leads to activation of Akt, but not the JNK or MAPK pathways {[26]-p(6359)}\n\n

* \n<br>*Src-phosphorylated EGFR Tyr920 can directly associate with p85 of PI3K [56]-p.37\n\n

*p85 subunit of PI3K binds to Y1035, Y1178, Y1203/05, Y1241, Y1257, Y1270 on ErbB3, and Y1056 on ErbB4. [23]\n\n

S_154 1 S_87 1 S_222 1 S_87 1 S_48 1 S_87 1 S_153 1 S_87 1 S_158 1 S_87 1 S_140 1 S_87 1 S_126 1 S_87 1 S_180 1 S_87 1 S_44 1 S_87 1 S_135 1 S_87 1 S_104 1 S_87 1 S_9 1 S_87 1 S_145 1 S_87 1 S_206 1 S_87 1 S_164 1 S_87 1 S_244 1 S_81 1 S_87 1

This node represents the ErbB2:ErbB4 heterodimer. It is activated by NRG AND ErbB2_Free AND ErbB4_Free.Due to the hierarchy in the activation of the various ErbB's, the activation of EGFR_ErbB2 occurs only when neither ErbB3_Free nor NRG are present (hence NRG functions as both positive and negative regulator).\n\n

*Neuregulins induce the formation of ErbB2_ErbB3 and ErbB2_ErbB4. [14]\n\n

ErbB2_ErbB4 is activated by ErbB2_Free, which represents inactive ErbB2 on the cell surface.\n\n

ErbB2_ErbB4 is activated by ErbB4_Free, which represents unliganded ErbB4 on the cell surface.\n\n

ErbB2:ErbB3 appears to be the most potent heterdimer and is predominant in carcinoma cells [12]. Therefore to capture this hierarchy in the ErbB signaling network, ErbB3_Free (AND NRG) will be a negative regulator to ErbB2_ErbB4.\n\n

S_107 1 S_117 1 S_125 1 S_31 1

TAK1 is activated by Tab1 and Tab2 [5, 6, 4, 3, 1]. To simplify the interactions, we have Tab_1_2 representing both forms of TAB. \n\n

*Tab interacts and induces kinase activity of TAK1 in intact cells {[5]-p(69)}\n<br>*TRAF6 binds MEKK1 and TAk1 via Tab2 {[6]-p(5)}\n<br>*Tab1 activates Tak1 by direct binding. {[4]-p(1)}\n<br>*Tab1 is essential for TAK1 kinase activity. Tab1 is sufficient for full activation of TAK1. {[3]-p(7360), [1]}\n<br>*Tab2 functions as an adaptor protein to recruit Tak1 to TRaf2 and Traf6, which leads to their interaction {[3]-p(7360)}\n<br>*Tak1 activation requires Tab1. {[4]-p(1)} \n<br>*Tab2 is also required for the phosphorylation and activation of TAK1, suggesting that Trafs are essential for the activity of TAK1. {[3]-p(7367)} \n<br>*Traf6 activates TAK1 {[2]-p(1), [7]-p(2)}\n

S_172 1

Gbg_i is an idealized Gbg that specifically binds Gai. Gbg_i is activated by the GPCR alpha-i_R when it is associated with Gai (i.e., when both Gai and Gbg_i are OFF). It is deactivated when Gas is GDP-bound (OFF) unless they are both OFF and alpha-i_R is ON. If Gai is ON, then Gbg_i is separated and is ON. {[8, 1, 9, 6, 7, 3, 2]} \n\n\n

S_201 1 S_67 1 S_222 1 S_201 1

CaM turns on CaMKK [2]. PKA turns off CaMKK, but CaM is dominant [1] so PKA drops out of the logic.\n\n

*CaM regulates CaMKK [2]\n<br>*CamKK can be potently activated by CaM-Ca complex {[1]-p(1)}\n\n

*PKA can phosphorylate two sites of CaMKK and inhibit its activity [1] Note, if Ca mobilization precedes elevation of cAMP levels, inhibition of CaMKK is reduced {[1]-p(4)}\n\n

S_3 1

AND_3_4 is positively regulated by Cas [2, 3, 4, 5, 1]. \n\n

S_129 1

Eps15 is activated by [[EGFR_Ub/Epithelial|EGFR_Ub]] OR [[EGFR_EGFR_EGF_PM/Epithelial|EGFR_EGFR_EGF_PM]] OR [[EGFR_EGFR_TGFa_PM/Epithelial|EGFR_EGFR_TGFa_PM]]. {[7, 4, 1, 2, 10, 9, 6]}\n\n

*Eps15 binds to EGFR ubiquitinated by Cbl. {[4]-p.8-9, [10]-p.910}\n<br>*Ubiquitinylation of EGFR establishes multiple attachment sites for proteins containing an ubiquitin-binding domain like Eps15 and epsin{[6]-p.349}{[9]-p.417} \n

*Eps15 is recruited by activated EGFR{[6]-p(349)}{[2]-p(567)}\n\n

*Eps15 is recruited and activated by EGFR{[6]-p(349)}{[2]-p(567)}{[7]-p(540)}\n<br>*Eps15 is phosphorylated and activated by EGFR {[1]-p(906)}\n\n

S_52 1 S_65 1 S_157 1

MEKK1 [8, 12, 5, 15, 7, 14, 2, 11, 1, 6] OR MEKK2 [5, 15, 14, 6, 11] OR MEKK3 [5, 15, 14, 6, 11] OR MEKK4 [5, 15, 14, 6, 1] OR MLK3 [12, 11, 5, 15, 14, 1, 11] OR MLK2 [5, 15, 1, 11] OR MLK1 [15, 10] OR Tlp2 [12, 5, 15, 14, 6, 3, 11, 16, 9] OR TAK1 [12, 5, 15, 14, 1, 11, 1] activate Sek1. ASK1 also activate Sek1 [12, 5, 15, 14, 11, 1, 4, 6], and since ASK1 is required for p38/SAPK activation, ASK1 will be in an AND with the other activators.\n\n

*ASK1 activates the SEK1 {[12]-p(4), [5]-p(33), [15]-p(822), [14]-p(2-Fig. 1), [11]-p(69), [1]-p(5), [4]-p(1), [6]-p(187), Fig. 1}\n<br>*ASK1 is necessary for the sustained activation of p38/SAPK, so it is likely necessary for Sek1 activation. {[13]-p(263)}\n

*MEKK2 can activate Sek1 {[5]-p(30, 33), [15]-p(822), [14]-p(2-Fig. 1), [6]-p(187), Fig. 1}\n<br>*Mekk2,in vitro, phosphorylates Mek and Sek1 {[11]-p(68)}\n\n

*MLK1 activates Sek1. {[15]-p(822), [10]-p(454)}\n\n

*MLK3 binds to phosphorylatyes SEK1 and MKK6, thereby activating both the SAPK and p38 pathways {[12]-p(3), [11]-p(70)}\n<br>*MLK3 activates Sek1 {[5]-p(33), [15]-p(822), [14]-p(2-Fig. 1), [1]-p(5)}\n<br>*In vitro, MLK2,3 phosphorylate and activate MKK4 {[11]-p(70)}\n\n

*MEKK4 can activate Sek1 {[5]-p(30, 33), [15]-p(822), [14]-p(2-Fig. 1), [6]-p(187), Fig. 1}\n<br>*MEKK4 is likely to activate SEK1 {[1]-p(5)}\n\n

*MLK2 activates Sek1 {[5]-p(33), [15]-p(822), [1]-p(5)}\n<br>*In vitro, MLK2,3 phosphorylate and activate MKK4 {[11]-p(70)}\n\n

*MKK4/7 is activated by MEKK1 {[8]-p(3-Fig. 1)}\n<br>*Sek1 is phosphorylated and activated by Mekk1 and MKK7 {[12]-p(3)}\n<br>*MEKK1 activates Sek1 {[5]-p(33), [15]-p(822), [7]-p(1), [14]-p(2-Fig. 1), [2]-p(2), [11]-p(68), [1]-p(5), [6]-p(187-Fig. 1)}\n\n

*TAK1 activates the SEK1 {[12]-p(4), [5]-p(30, 33), [15]-p(822), [14]-p(2-Fig. 1), [1]-p(5)}\n<br>*In vitro, TAK1 phosphorylates MKK4 and MKK6, but not MKK1 {[11]-p(69)}\n<br>*Tak1 activates SEK1 independent of MEKK1 and MLK3 {[1]-p(5)}\n\n

*MEKK3 can activate Sek1 {[5]-p(30, 33), [15]-p(822), [14]-p(2-Fig. 1), [6]-p(187), Fig. 1}\n<br>*Mekk3,in vitro, phosphorylates Mek,Sek1 and MKK3 {[11]-p(68)}\n\n

S_49 1 S_236 1 S_120 1 S_236 1 S_221 1 S_236 1 S_146 1 S_236 1 S_42 1 S_236 1 S_204 1 S_236 1 S_6 1 S_236 1 S_216 1 S_236 1 S_150 1 S_236 1

This node represents the homodimer of EGFR activated by EGF on the early endosome. CCVs containing EGFR complexes rapidly release their coat and fuse with early endosomes.{[6]} Uncoating of coated vesicles by [[GAK/Epithelial|GAK]] and [[Hsc70/Epithelial|Hsc70]] allows for homotypic fusion in a Rab5-dependent and EEA1-dependent manner to form early endosomes{[11, 9]}. Therefore, EGFR_EGFR_EGF_End is activated by ([[EGFR_EGFR_EGF_CCV/Epithelial|EGFR_EGFR_EGF_CCV]] AND [[EEA1/Epithelial|EEA1]] AND [[Rab5/Epithelial|Rab5]] AND [[PIP3_345]] AND [[Hsc70/Epithelial|Hsc70]] AND [[Rabaptin_5/Epithelial|Rabaptin_5]] AND [[GAK/Epithelial|GAK]]). Endocytosed EGFR in early endosomes will be either recycled back to the plasma membrane in active form (fast recycling) which results in activation of [[EGFR_EGFR_EGF_FR/Epithelial|EGFR_EGFR_EGF_FR]] or go to sorting endosomes, activating [[EGFR_EGFR_EGF_MVB/Epithelial|EGFR_EGFR_EGF_MVB]]. If the fast recycling happens, it will turn of EGFR_EGFR_EGF_End to indicate it. This inactivation only happens if EGFR_EGFR_EGF_End was on previously, and is not dominant to positive regulators. Because PKC and cortactin inhibit fast recycling, when these species are on, the PM localization of EGFR therefore will not deactivate the endosomal localization of EGFR. For for the latter case, EGFR_EGFR_EGF_MVB acts as a negative regulator of EGFR_EGFR_EGF_End. Both negative regulators (EGFR_EGFR_EGF_PM and EGFR_EGFR_EGF_MVB) are only effective when EGFR was already in endosome (i.e., EGFR_EGFR_EGF_End was ON).\n\n

*Activaton of EGFR_EGFR_EGF_MVB results in removing (i.e., turns off) EGFR_EGFR_EGF_End.\n\n

*Rabaptin_5 is required for the fusion of CCVs with early endosomes.{[17]-p(1941)} \n\n

*CCVs undergo uncoating in a process mediated by auxilin (GAK) and Hsc70, which is essential for CCVs fusing with early endosomes.{[7]-p(351)}{[8]-p(31.8)} \n\n

*CCVs undergo uncoating in a process mediated by auxilin (GAK) and Hsc70, which is essential for CCVs fusing with early endosomes.{[7]-p(351)}{[8]-p(31.8)} \n<br>*GAK supports the uncoating of clathrin from CCVs.{[5]-p(641)} \n\n

*For the association of EEA1 with the endosome membrane, the concomitant presence of both Rab5 and PIP3_45 is crucial.{[4]-p(3748)}{[11]-p(599)}\n\n

*EEA1 is required for the fusion between EE and CCVs.{[4]-p(3747)} \n\n

*EGFR_EGFR_EGF_End is activated by EGFR_EGFR_EGF_CCV, which represents dymerized and activated EGFR in a clathrin-coated vesicle.\n\n

*Rab5 is necessary on both CCVs and early endosomes for a fusion event to occur.{[4]-p(3745, 3746)}{[2]-p(3)}{[11]-p(599)} \n<br>*Rab5 promotes endosome fusion by recruiting cytosolic components of the fusion apparatus.{[1]-p(697)} \n<br>*Rab5 is required for targeting and fusion of endocytic vesicles to early endosomes.{[15]-p(27)} \n\n

S_29 1 S_70 1 S_210 1 S_11 1 S_74 1 S_115 1 S_192 1 S_16 1 S_227 1 S_16 1

PKA is a negative regulator [1, 11], and we are making it dominant (except when GDI is OFF) because it works through phosphorylation that enhances GDI binding [11, 16, 9]. Graf [6, 4], p190RhoGap [19, 15, 17, 32, 21, 8, 27, 20, 23, 30], and RhoGDI [28, 5, 31, 25, 29, 8, 13] are negative regulators as well. If {p190RhoGap OR Graf are ON} AND Rho is ON, Rho will be OFF because they are both Gaps. If {Graf OR p190RhoGap are ON} AND RhoGDI is ON AND Rho is OFF, Rho will be OFF because Rho GDI will keep Rho in the GDP bound state. In the absence of the negative regulators, RhoGEF will turn Rho ON [19, 25, 22, 14]. In the absence of neg. regulators, if Rho is ON, it will stay ON.\n\n

*Graf is bound to Fak to inhibit activity of Rho {[15]-p(14), Fig. 7}\n<br>*Graf is a GAP for Rho {[6]-p(1)}\n<br>*Graf is a GAP for Cdc42 and Rac {[4]-p(9576)}\n\n

*p120 catenin binds to RhoA and maintains it in GDP-bound state {[7]-p.13}\n<br>*''in vitro'', p120_catenin binds to RhoA-GDP and sequesters it from activation {[34]-p.663}\n<br>*p120_catenin functions as a RhoGDI, thus preventing Rho from binding GTP and becoming active. [26]\n

*PKA can directly phosphorylated the C terminus of RhoA , resulting in an increased binding to RhoGDI and therby terminate RhoA activity {[11]-p(577), [16]-all, [9]-p(275)}\n<br>*Rho can be directly phosphorylated by PKA at Ser188 near its C-terminus and inhibit Rho function {[1]-p(164)}\n\n

*Rho is positively and negatively regulated by RhoGEF and p190RhoGAP,respectively. {[19]-p(7)}\n<br>*Rho is inhibited by RhoGAP {[15]-p(14), Fig. 7, [17]-p(9)}\n<br>*Integrin mediated cell-matrix adgesion inactivates RhoA in a Src-dependent fashion via the tyrosine phosphorylation of p190GAP {[32]-p(9)}\n<br>*RhoGap binds to Rho and stimulates GTPase activity. {[21]-p(2)}\n<br>*Rho is regulated by RhoGap. {[8]-p(1)}\n<br>*p190RhoGAP can catalyze hydrolysis of Rho A,B, and C equally well but works with weakly on Rac or Cdc42 {[27]-p(2)}\n<br>*p190RhoGAP is a negative regulator of Rho activity {[20]-p(584), Fig. 2, [23]-p(7939)}\n<br>*activation of p190 RhoGAP results in inhibition of RhoA {[30]-p(125)}\n\n

*RhoGDI is a GAP for Rho and inhibits its activity {[28]-p(158)}\n<br>*RhoGDI binds to Rho to maintain its GDP state until it's removed from cytosol.The mechanism unknown {[28]-p(165, 167), [33]-p(3), [31]-p(5)}. ->Might have a significant effect on our logic.\n<br>*RhoGDI interacts specifically with GDP Rho and inhibits the dissociation of GDP from Rho. {[25]-p(462), [29]-p(1)}\n<br>*Rho GDI prevents GDP Rho binding to cell membranes, but not GTP Rho. {[25]-p(463), [29]-p(1)}\n<br>*Rho is regulated by RhoGDI {[8]-p(2)}\n<br>*RhoGDI was originally observed to regulated the dissociation of GDP from Rho {[2]-p(26206)}\n<br>*RhoGDI acts as a ngeative regulator by inhibiting the activation of Rho family GTP binding proteins. {[13]-p(1)}\n<br>*RhoGDI exhibits stimulated release of Rho-related GTP binding proteins from membranes. {[13]-p(1)}\n\n

S_242 1 S_90 1 S_228 1 S_205 1 S_228 1 S_71 1 S_133 1 S_199 1

Ca is turned ON when IP3R is ON [12, 14, 2, 7, 1, 5, 8, 3, 4, 9, 13, 10, 6]. Ca is turned OFF by external calcium pump (ExtPmp; [11]). We will make negative regulation by the pump dominant.\n\n

S_98 1 S_152 1

RIN is activated by Ras.[1]\n\n\n

*Ras activates RIN [1]\n

S_44 1

S_67 1 S_22 1

CALM is activated by the localization at the plasma membrane by PIP2_45.{[1]-(p.3)}\n\n

*PIP2_45 targets CALM to the plasma membrane.{[1]-(p.3)}\n<br>*PIP2_45 interacts with CALM/AP180.{[4]-(p.159)}\n<br>*CALM binds to PIP2_45 as well as clathrin and AP2.{[3]-(p.3235)}{[2]-(p.3235)}.\n\n\n

S_118 1

S_168 1 S_237 1

Mek activates Erk [24, 34, 72, 27, 10, 11, 43, 50, 30, 40, 53, 54, 9, 28, 55, 71, 45, 47, 23, 36, 66, 33, 21, 57, 42, 1, 46, 48, 64].\nPP2A is a negative regulator [51, 41, 5, 45, 30, 42, 62, 70, 63, 15, 37]\nMKPs are negative regulators [51, 28, 61, 30, 62, 70, 36, 19, 8, 56].\nAs far as dominance; if Erk is ON, then Mek is dominant to the negative regulators. If Erk is OFF, Mek is also dominant. If Erk is ON and everything else[pos. and negative] is OFF, Erk stays ON by itself.\n\n

*MEK as an upstream of Erk {[24]-p(2-Fig. 1), []-p(3), [34]-p(5-Fig. 1), [72]-p(2-Fig. 1), [27]-p(5-Fig. 1), [10]-p(3-Fig. 1), [11]-p(1), [43]-p(1), [50]-p(3-Fig. 2), [30]-p(480, 483), [40]-p(41-Fig.6), [53]-p(2-Fig. 1), [54]-p(3)}\r\n<br>*Erk is phosphorylated by MEK {[9]-p(6), [28]-p(1), [55]-p(2), [71]-p(161), [45]-p(100), [47]-p(2), [23]-p(2), [36]-p(1), [66]-p(1), [33]-p(276), []-p(2)}\r\n<br>*Erk's threonine and tyrosine residues are phosphorylated by MEK {[21]-p(1)}\r\n<br>*MEK1/2 stimulates Erk. {[57]-p(822)}\r\n<br>*MEK is an immediate upstream activator of Erk {[42]-p(4), [1]-p(234)}\r\n<br>*Erk1/2 is phosphorylated and activated by MEK1/2 {[46]-p(1), [48]-p(2-Fig. 1), [64]-p(1), [8]-p(187-Fig. 1), [25]-p(357)}\r\n<br>*Mek1 and Mek2 are upstream phosphorylators and activators of Erk1 and Erk2. {[19]-p(1)} \r\n<br>*Erk binds to MEK-1. {[19]-p(5)}\r\n<br>*MEK is a dual specifcity kinase that phosphorylates (activates) Erk {[52]-p(1,2), [31]-p(322)}\r\n<br>*Mek phosphorylates and stimulates Erk. {[32]-p(1)}\r\n<br>*MEK specifically activates Erk {[65]-p(2), []-p(2)}\r\n<br>*Mek1 and inactivator MKP3 bind to same site on Erk2. {[22]-p(198)}\r\n<br>*Only Mek1 and Mek2 can activate Erk2. {[22]-p(200)}\r\n<br>*Mek1/2 phosphorylates and activates Erk. {[49]-p(2, 3)}\r\n<br>*Raf promotes phosphorylation of Mek, which in turn is required to activate Erk by phosphorylation. {[15]-p(1)}\r\n<br>*MEK phosphorylates Erk, which leads to its activation {[3]-p(1)}\r\n<br>*Raf propagates signals by activation the dual specifity kinase Mek1, which in turn activates Erk1/2. {[67]-p(1)}\r\n\r\n

*PP2A can dephosphorylate MEK1 and ERK-family kinases {[51]-p(3), [41]-p(1), [5]-p(428)}\n<br>*PP2A dephosphorylates and inactivates ERK {[45]-p(99), [30]-p(484), [42]-p(1)}\n<br>*PP2A inactivates Erk in cytoplasm {[62]-p(3-Fig. 1), [70]-p(76)} \n<br>*PP2A and PP1 can inactivate ERK1/2 and MEK1/2 {[70]-p(80)}\n<br>*PP2A and PTP1b can dephosphorylate and inactivate Erk {[63]-p(2)}\n<br>*PP2A coordinates membrane recruitment of Ksr_Mek complex and the activation of Raf through dephosphorylation of a common 14-3-3 binding site. Both steps are required for activation of Mek and the subsequent activation of Erk. {[15]-p(2)}\n<br>*Mek and Erk are likely candidates for the inhibitory effect of PP2A, given that both kinases can be dephosphorylated and inactivated by PP2A in vitra, and that the inhibition of PP2A leads to Mek and Erk activation in vivo. {[37]-p(5)}\n\n

*MKPs are upregulated upon Erk's activation and forms a negative feedback loop. {[51]-p(3, 4)} Q:Do PP2A and MKPs both have to be inactivating Erk to actually inactivate it? \n<br>*MKP can be induced by Erk to inhibit SAPK and p38 signal transduction or, alternatively it can be induced by SAPK or p38 activation to dephosphorylate Erk {[28]-p(5)}\n<br>*MKPs dephosphorylate Erk {[61]-p(5), [30]-p(484)}\n<br>*MKP-1 dephosphorylates Erk in vivo and in vitro {[62]-p(2), [70]-p(78)}\n<br>*Erks can be inhibited by MKPS {[36]-p(4)}\n<br>*MKP-1 dephosphorylates and inactivates ERK. {[19]-p(2)}\n<br>*low concentrations of MKP-3 completely inactivate ERK1 and ERK2. MKP-4 is effective at inactivating ERK. MKP-3 binding to ERK is direct. {[19]-p(4)}\n<br>*MKP-3 is Erk-specific {[62]-p(3), [70]-p(76)}; It cannot dephosphorylate p38 or SAPK {[62]-p(3)}\n<br>*MKPs 1, 2 and 4 inactivate Erk, p38, and SAPK {[70]-p(76, 78)} \n<br>*MKP1 and MKP2 are induced upon activation ERK activation, and stabilized by ERK phosphorylation. {[]-p(3)}\n<br>*MKP1 is phosphorylated by ERK {[]-p(3)}\n<br>*MKP3 and MKP1 are cataylitically activated upon ERK binding. {[]-p(3)}\n<br>*MKP1 and MKP2 are good candidates for Erk inactivation: they are induced by Erk activation, posses Erk docking sites, and are inhibited by tryosine phosphatase specific inhibitors. {[]-p(3)}\n<br>*all of nine members of dual-specificity MKPs are able to dephosphorylate both the threonine and tyronsine residues on ERK2 both in vitro and in vivo {[8]-p(187), Table 1}\n<br>*Erk1,2 can be inhibited by MKP {[69]-Fig. 3}\n\n

S_234 1 S_147 1 S_43 1 S_142 1

Src can negatively regulate beta-catenin. In addition, EGFR also negatively regulates beta-catenin. [5, 7, 6]. Thus all dimers of EGFR (EGFR_ErbB2, EGFR_ErbB3, EGFR_ErbB4) will be negative regulators. Furthermore, because EGFR signaling continues while EGFR is being internalized [4], the following localizations of EGFR will also be regulators of B_catenin: EGFR_EGFR_EGF_PM, EGFR_EGFR_EGF_CCP, EGFR_EGFR_EGF_CCV, EGFR_EGFR_EGF_End, EGFR_EGFR_EGF_MVB, EGFR_EGFR_TGFa_PM, EGFR_EGFR_TGFa_CCP, EGFR_EGFR_TGFa_CCV, EGFR_EGFR_TGFa_End, and EGFR_EGFR. Fer AND PTP1b are positive regulators that counteract the neg. regulation, thus they are dominant to the negative regulatory mechanism [7, 6].\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Src phosphorylates beta-catenin (Y654) lowering its affinity for [[E-cadherin]]-binding {[5]-p.663,[7]-p.49, [6]-p.461, [2]-p.2287}.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

*Fer_activated PTP1B dephosphorylates beta-catenin on Y654 which serves as a balancing mechanism when external stimuli are not present, and lowers its affinity for cadherins {[7]-p.49}\n<br>*PTP1B binding to beta-catenin is dependent on the previous phosphorylation of Y152 (by Fer Kinase). Loss of Fer from N-cadherin also results in the loss of binding ability of PTP1B (and beta-catenin, and p120_catenin) {[6]-p.462}. \n<br>*Active PTP1b is able to rescue the loss of cadherin complex upon beta-catenin phosphorylation by Src and EGFR, and maintain the dephosphorylated state of beta-catenin {[6]-p.463,fig.2}.\n

*EGFR phosphorylates beta-catenin (Y654) lowering its affinity for E-cadherin-binding {[5]-p.663,[7]-p.49, [6]-p.461,[2]-p.2287}. Therefore all localizations of EGFR will regulate B_catenin.\n\n

*see EGFR_EGFR_EGF_PM above.\n\n

S_79 1 S_16 1 S_157 1 S_30 1 S_227 1 S_244 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_58 1 S_79 1 S_16 1 S_157 1 S_30 1 S_227 1 S_244 1 S_214 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1 S_16 1 S_157 1 S_30 1 S_227 1 S_244 1 S_214 1 S_58 1 S_79 1 S_52 1 S_174 1 S_195 1 S_99 1 S_66 1 S_194 1 S_29 1 S_139 1

S_28 1

S_220 1 S_233 1 S_237 1 S_91 1 S_233 1 S_237 1 S_195 1 S_233 1 S_237 1

Fak [9] OR Src [13] are negative regulators of p120Gap, and we are making them dominant. Ca [3, 16], PIP2_45, PIP2_34, and PIP3_345 [16], and EGFR_Y992 [2] all can localize p120RasGap to the membrane, which is required since its Gap activity is constitutively on. We are putting them all in an OR. \n\n

*Src is a negative regulator of p120GAP. {[13]-p(3278)}\n\n

*Fak overexpression facilitated the SH2-mediated binding and sequestering of p120RasGAP, which diminished the association of p120GAP and Ras, leading to Ras activation {[9]-p(62)}\n\n

*GAP interacts with negatively charged phospholipids which can activate GAP. {[16]-p(552)}\n<br>*p120Gap binds to PIP2_45 and to the products of PI3K. {[16]-p(558)}\n\n

*RasGAP interact with EGFR at the phosphorylated Y992 [1]\n<br>*p120RasGAP needs to interact with EGFR and PDGF receptor to stimulate hydrolysis on Ras {[2]-p(25)}\n<br>*p120Gap complexes with RTK's that are believed to bring them to the membrane surface (and are required for full GAP activity). {[16]-p(552)}\n\n\n

*see PIP2_45 above.\n\n

*see PIP2_45 above.\n\n\n

S_54 1 S_135 1 S_244 1 S_170 1 S_135 1 S_244 1 S_118 1 S_135 1 S_244 1 S_74 1 S_135 1 S_244 1

TAK1 [8, 7, 12, 4, 9] OR MEKK4 [4, 6] OR MLK3 [10, 12, 2] OR PAK [6, 3] OR TAO_1_2 [14] OR Tpl2 [6] can activate MKK6. ASK1 can also activate MKK6 [8, 10, 12, 4, 1, 15, 5, 6], and since ASK1 is required for p38/SAPK activation, ASK1 will be in an AND with the other activators. \n\n

*MKK6 is activated by ASK1 {[8]-(p(3), Fig. 1), [10]-p(4), [12]-p(2-Fig.1)}\n<br>*ASK1 can activate MKK6 {[4]-p(33), [1]-p(1059)}\n<br>*ASK1 phosphorylates and activates MKK4 or MKK7 and MKK3 or MKK6 {[15]-p(893, 897), [5]-p(1), [6]-p(187), Fig. 1}\n<br>*ASK1 is necessary for the sustained activation of p38/SAPK, so it is likely necessary for MKK6 activation. {[11]-p(263)}\n\n

*Pak is displayed as an activator of MKK3 and MKK6 {[12]-p(2-Fig. 1), [6]-p(187), Fig. 1}\n\n

*MLK3 binds to phosphorylatyes SEK1 and MKK6, thereby activationg both the SAPK and p38 pathways {[10]-p(3)}\n<br>*MLK3 activates MKK6 {[12]-p(2-Fig. 1), [2]-p(6)}\n\n

* \n<br>*Mekk4 can activate MKK3 {[4]-p(33), [6]-p(187), Fig. 1}\n\n

*TAO_1_2 can activate MKK3. {[14]-all} \n\n

*MKK6 is activated by TAK1 {[8]-(p(3), Fig. 1), [7]-p(1), [12]-p(2-Fig.1)}\n<br>*TAK can activate MKK6 {[4]-p(33)}\n<br>*In vitro, TAK1 phosphorylates MKK4 and MKK6, but not MKK1 {[9]-p(69)}\n\n

S_204 1 S_236 1 S_21 1 S_236 1 S_97 1 S_236 1 S_146 1 S_236 1 S_221 1 S_236 1 S_150 1 S_236 1

DAG activates PKC [41, 47, 27, 14, 26, 22, 34, 10, 9, 13, 35, 24, 4, 32, 37, 17, 3, 36, 46, 21, 30]. Ca can activate PKC [6, 23, 35, 48, 15, 24, 5]. These two are an AND relation. PDK1 is associated with activation of PKC [9, 32, 42, 28, 25, 2, 31, 38], but it appears that PDK1 is necessary but not sufficient to activate inactive PKC [, 32], but only if PKC was not ON before [25, 30]. AA is in an OR with DAG (our decision based on the mechanism). PP2A [20, 12, 24] and Trx [7, 39] are negative regulators. PP2A inactivates PKC if PKC is ON, but the positive regulators are dominant to PP2A. Trx is made to be dominant when PKC is ON. \nNote, that PKC has been divided into two nodes to represent a closer physiological behaviour. PKC_primed has to be primed by PDK1 first and after then, PKC can be activated in presence of (Ca AND DAG) OR AA as mentioned above. \n\n

*PKC has been shown to be activated by Trx (wrong connection in the network?) {[7]-p(2)}\n<br>*Trx inhibits autophosphorylation and histone phosphorylation of PKC {[39]-p(194)}\n\n

*PKC is inactivated by PP2A {[20]-p(3), [12]-p(428)}\n<br>*PKC can form a complex with PP2A {[24]-p(5)}\n<br>*PP2A may be required for dephosphorylation of PKC substrates or, indeed, PKC itself {[24]-p(6)}\n\n

*PKC is a downstream pathway from DAG {[41]-p(5), Fig. 3, [47]-p(2), [27]-p(2), Fig. 1}\n<br>*PKC is activated by DAG and PDK1 {[14]-p(2)}\n<br>*Binding of DAG to PKC isoforms results in PKC activation. {[26]-p(1)}\n<br>*Activation of PKC is promoted by DAG {[22]-p.2(282), [34]-p(502), [10]-p(187)} \n<br>*Mobilized Ca causes PKC to bind to the cytosolic leaf of the plasma membrane, where it is activated by DAG {[6]-p(261)}\n<br>*Many isoforms of conventional PKC are stimulated by Ca and DAG {[23]-p(3), [48]-p(235)}\n<br>*PKC is activated by DAG {[9]-p(1), [13]-p(1, 2), [35]-p(4), [24]-p(3), [4]-p(6), [32]-p(968, 992), [40]-p(139), [48]-p(236)}\n<br>*Ca released into cytosol,together with DAG can activate PKC {[15]-p(2)}\n<br>*DAG directly binds to and activates the PKC {[37]-p(765), [17]-p(3)}\n<br>*DAG can activate PKC {[3]-p(1), [36]-p(1), [46]-p(1), [21]-p(6)}\n<br>*PKC is a chief direct target for the actions of DAG {[30]-p(1)}\n<br>*Conventional PKCs regulation is through DAG and Ca2+. In contrast, novel PKCs are regulated by DAG but not in a Ca2+ dependent manner, these proteins lack the Ca2+ binding domain. {[33]-p(1), [31]-p(1)}\n<br>*While all DAG species can activate PKC in vitro, it is only the polyunsaturated DAGs which can do so in intact cells {[48]-p(240)}\n\n

*Mobilized Ca causes PKC to bind to the cytosolic leaf of the plasma membrane, where it is activated by DAG {[6]-p(261)}\n<br>*Many isoforms of conventional PKC are stimulated by Ca and DAG {[23]-p(3), [35]-p(4), [48]-p(235)}\n<br>*Ca released into cytosol,together with DAG can activate PKC {[15]-p(2), [24]-p(3)}\n<br>*Ca directly activates PKC, providing a positive feedback loop {[5]-p(445)}\n<br>*Ca directly activates PKC, providing a positive feedback loop. {[5]-p(445)}\n\n

S_182 1 S_84 1 S_229 1 S_28 1 S_240 1 S_240 1 S_43 1 S_28 1 S_28 1 S_240 1 S_18 1 S_84 1 S_229 1 S_28 1 S_240 1

The activator of Gas is the GPCR alpha-s_R [17, 1, 3, 12, 11]. Gbg_is a GDI for Gas, which keeps Gas OFF when it is OFF [7, 9, 8, 12]. PKA is a negative regulator [5, 1, 13], as is RGS [10, 6, 2, 15, 18, 12].\nGas is activated by alpha-s_R when Gas is OFF AND Gbg_is OFF AND PKA is OFF [1, 7, 9, 8, 5, 11, 13].\nGas is deactivated by RGS when Gas is GTP-bound (i.e., ON) [10, 6, 2, 4, 12]. Although PKA is a negative regulator, it only affects the initial activation of Gas, so PKA only affects Gas when Gas is OFF [5, 1, 11, 13]. We are requiring RGS to stimulate the GTPase activity of Gas, so if Gas is ON and RGS is OFF, Gas will stay on even in the absence of alpha-s_R activation (unless there is an initial condition of Gbg_s OFF) otherwise, RGS would simply drop out of the logic. \n\n

*RGS functions as a GAP toward Ga subunits but not Gbg {[10]-p.1,[6]-p(2)}\n<br>*RGS binds to Gas to stop its activity {[2]-p.529}\n<br>*Deactivation of Gas can be accelerated by RGS that server as a GAP. {[4]-p(3)}\n<br>*RGS is a GAP for Ga {[15]-p(1)}\n<br>*RGS2 is not a GAP for Gas, but has been show to bind to some isoforms of AC to inhibit catalitic activity {[15]-p(2)}\n<br>*Many RGS proteins catalyze reapid GTP hydrolysis by isolated Ga subunits in vitro and attenuate agonist/GPCR_stimulated cellular responses in vivo {[12]-p(551)}\n\n

S_55 1 S_5 1 S_133 1 S_241 1 S_5 1 S_156 1 S_241 1

PIP3_345 is necessary for p115RhoGEF [13, 15, 14, 12]. Ga12/13 is also necessary [15, 8, 14, 12, 3, 5, 4]. Neither is sufficient, so they are in an AND relation. \n\n

S_197 1 S_74 1

Ras is a positive regulator of RalGDS, probably by attracting it to the membrane [20, 4, 14, 10, 12, 16, 7, 13, 17, 18, 1, 15, 2, 6, 11]. Once at the membrane, interaction with PDK1 releases an auto-inhibition [2]. While there is some data indicating that Ras is sufficient for RalGDS activation, that may be an artifact due to overexpression [2], so we will have Ras and PDK1 in an AND. PIP3_345 will be an input for RalGDS to indicate that the PDK1 interaction happens at the membrane (see information for PDK1). Phosphorylation by PKC is a suppressor of RalGDS [2], and it will be made dominant.\nA second pathway to activate RalGDS involves the GPCRs (alpha-s_R, alpha-q_R, alpha-i_R). RalGDS is associated with B_Arrestin which keeps it OFF [9]. GPCR removes the B-arrestin and the GPCR attracts RalGDS to the membrane [9]. Therefore, these are in an AND relation.\nEither pathway will be sufficient to activate RalGDS. \n\n\n

*RalGDS is affected by Ras {[20]-p(2), [4]-p(162), Fig. 4, [14], [10]-p(2-Fig. 1, 3-Fig. 2), [11]-p(205)}\n<br>*RalGDS is downstream of Ras {[12]-p(8), [16]-p(2)}\n<br>*RalGDS is activated by Ras {[7]-p(2), Fig. 1, [13]-p(162), [17]-p(3), Fig. 2, [18]-p(8), [1]-p(1)}\n<br>*H-Ras activates RalGDS {[15]-p(1)}\n<br>*Ras bind to and activates RalGDS. {[2]-p(1)}\n<br>*Ras binding to RalGDS was sufficient for activating RalGDS. {[2]-p(1)}\n<br>*Ras relocalizes RalGDS to the membrane {[2]-p(1)}\n<br>*Ras activates Ral through the activation of RalGDES {[6]-p(357)}\n

S_67 1 S_95 1 S_44 1 S_74 1 S_128 1 S_240 1 S_213 1 S_95 1 S_44 1 S_74 1 S_128 1 S_240 1 S_55 1 S_95 1 S_44 1 S_74 1 S_128 1 S_240 1 S_24 1 S_95 1 S_44 1 S_74 1 S_128 1 S_240 1

PTPa is a Src activator when Src is phosphorylated on Tyr527 (i.e. OFF)[13, 46, 55, 20, 41]. Cas [17, 36, 22] and PTP1b [49, 14, 55] and Fak [15, 35, 43, 39, 13, 12, 32, 8, 17, 20, 28, 25, 38, 10, 3, 27] are positive regulators. The activation logic is following: (PTP1b AND Cas) OR (Fak AND PTP1b) [27, 14]. Another way to activate Src is through B_Arrestin [19, 15, 2, 9, 54] AND (alpha-s_R [26, 50, 35, 54] OR Gai [40, 45, 27, 54] OR Gas [27, 45, 17, 54].\nCsk is a negative regulator which inactivates Src when Src is ON [5, 44, 27, 39, 6, 18, 17, 23, 35, 11, 24, 53, 13, 51, 25, 54, 20, 9, 55]. \n\n

*Beta arrestin regulates Src {[19]-p(5)}\n<br>*B-arrestin activates Src. This interaction leads to GPCR mediated activation of MAPK {[15]-p(6)}\n<br>*Barrestin1 interacts with catalytic domain of c-Src and up-regulates it actions {[2]-p(268)}\n<br>*Stimulation of GPCR recruits B-arrestin, and B-a brings with it activated src. Blocking the B-arr_src interaction blocks GPCR from stimulating Erk (through EGFR). {[9]-p(1535, 1536)}\n<br>*Src family kinase can bind to arrestins which confers tyrosine kinase activity upon a complex assembled on the desensitexed GPCR {[54]-p(7971), Fig. 1}\n\n

*p130Cas can activate src by direct binding {[17]-p(30)}\n<br>*p130Cas has recently been shown to associate with and stimulate c-Src activity {[36]-p(7986)}\n<br>*Cas can interact with Fak. {[22]-p(3)}\n\n

*Gai and Gas activate Src {[27]-p.4(459), [45]-p(5), [17]-p(30, 34)}\n<br>*Gas may directly activate Src {[45]-p(5)}\n<br>*In vitro, GTP-gS-bound Gas and Gai phosphorylate Src at Tyr_530 results in significant activation of kinase {[54]-p(7971)}\n\n

*Src is activated by Gai {[40]-(p.8(348),Fig. 9), [45]-p(2)}\n<br>*Gai and Gas activate Src {[27]-p.4(459), [45]-p(5), []-p(17176)}\n<br>*In vitro, GTP-gS-bound Gas and Gai phosphorylate Src at Tyr_530 results in significant activation of kinase {[54]-p(7971)}\n\n

*FAK activates Src {[15]-p(3), [35]-p.18(138), [43]-p(1)}\n<br>*Src can be activated independently of FAK, but FAK-dependent pathway is required for maximal stimulation of Src activity. {[39]-p(8)}\n<br>*Src is bound to FAK {[39]-p(5), Fig. 3}\n<br>*Src is activated by FAK -> inactive Src can be recruited into complex with FAK. {[39]-p(9), Fig. 4}\n<br>*Src activity is enhanced by FAK {[13]-p(443, 445)}\n<br>*Src is activated upon binding to FAK. {[12]-p(3)}\n<br>*Src is phosphorylated by itstelf or FAK {[32]-p(8)}\n<br>*Fak competes with Src tail for binding to y527=src is activated. {[17]-p(30)}\n<br>*Src is recruited by FAK {[8]-p(1)}\n<br>*FAK and Sin-1(a p130CAS-related protein) have been shown to activate Src by disruption of the intramolecular inhibitory interactions {[20]-p(7932)}\n\n

*Inhibitor of Src in L cells - too specific?How about other cells?\n<br>*PTP1b ACTIVATES src by de-phos. the csk site. {[49]-p(313)}\n<br>*Src is substrate of PTP1b {[]-table 1}\n<br>*Src can be activated by PTP1b {[]-p(2327)}\n<br>*Overexpression of a catalytically defective mutant of PTP1B in mouse L cells reduces Src activity when the cells are plated on fibronection {[20]-p(7931)}\n<br>*Src is activated by PTP1b because it dephosphorylates Src at Y527 (an inhibitory phosphorylation site). {[14]-p(6)}\n<br>*Src is dephosphorylated (and activated) by PTP1B only when Cas is present to bring them together. {[14]-p(8)}\n<br>*PTP1b, Shp2, PTPa dephosphorylate Tyr527 of Src, leading to the activation of Src {[55]-p(4, 7)}\n\n

*Autophosphorylated (Y992, Y1086, Y1148) as well as phosphorylated Y1101 residues can bind to and activate Src [17]\n

*Autophosphorylated (Y992, Y1086, Y1148) as well as phosphorylated Y1101 residues can bind to and activate Src [17]\n<br>*EGFR autophosphorylates, attracts and activates src, which then phosphorylates EGFR. The src phos. of EGFR greatly enhances EGFR activity. {[17]-p(32)}\n<br>*EGF stimulation results in the activation of the Src protein-tyrosine kinase {[42]-p(24967)}\n<br>*Src is recruited by transactivated EGFR {[50]-p(2)}\n<br>*Src is activated in response to growth factors such as PDGF, which induces PDFGR autophosphorylation {[56]-p(4)}\n<br>*Src is an effector of EGFR {[]-p(3)}\n<br>*Integrin and EGFR receptors cluster by integrin ligand, forming complexes dependent on Src. {[7]-p(1)}\n<br>*When EGF stimulates EGFR, Src is recruited. {[9]-p(1532)}\n\n

*Csk - inhibitor of Src {[5]-p(2), [44]-p(1), [27]-p(457), [39]-p(7), [6]-p(2), [18]-p(3), [17]-p(30), []-p(17170, 17176, Fig. 7), [33]-p(2), [23]-p(1-Fig. 1)}\n<br>*Csk phosphorylates Src {[35]-p(131)} and by binding to PAX or FAK, Csk could inhibit Src {[35]-p.13(133)}\n<br>*Csk phosphorylates Src on Y527, possibly leading to inhibition of Src activity {[11]-p(533)}\n<br>*Csk phosphorylates Src to inactivate it {[24]-p(3), [53]-p(9)}\n<br>*CSK inhibits Src activity {[13]-p(460)}\n<br>*Csk downregultates Src {[53]-p(8)}\n<br>*Csk inhibits Src by phosphorylating its TyrT {[51]-p(1)}\n<br>*Csk is a negative regulator of Src {[25]-p(123)}\n<br>*CSK phosphorylates Src at Tyr_530 and promotes pY-530 binding to the SH2 domain and suppresses the catalytic activity of teh enzyme {[54]-p(7971)}\n<br>*Csk can catalyze the phosphorylation of a carboxy-terminal tyrosine residue which can negatively regulate SFKs {[20]-p(7931)}\n<br>*Csk has a negative role in the regulation of Src-family PTK {[]-p(18)}\n<br>*CSK blocks the ability of Gbg to stimulate phosphorylation of EGFR and Shc {[9]-p(1535)}\n<br>*Csk phosphorylates Src at Tyr527 and inhibits Src {[55]-p(3), [27]-p(457)}\n\n

*Autophosphorylated (Y992, Y1086, Y1148) as well as phosphorylated Y1101 residues can bind to and activate Src [17]\n\n

*PTPa promotes Src activity {[13, 17]-p(455)}\n<br>*PTPa is a regulator of Src {[46]-p(1)} and is capable of Src activation {[46]-p(3)}\n<br>*PTPa dephosphorylates tyrosine-527 in Src and activates it {[25]-p(123), [55]-p(9, 10)}\n<br>*Src can be activated by PTPa {[]-p(2327)}\n<br>*PTPa overexpression has been shown to activate Src in vivo {[20]-p(7931)}\n<br>*PTP1b, Shp2, PTPa dephosphorylate Tyr527 of Src, leading to the activation of Src {[55]-p(4)}\n<br>*PTPa has to be dissociated from Grb2 to dephosphorylate Src {[55]-p(10), [41]}\n\n

S_241 1 S_95 1 S_60 1 S_244 1 S_135 1 S_79 1 S_60 1 S_244 1 S_129 1 S_79 1 S_60 1 S_244 1 S_167 1 S_60 1 S_244 1 S_55 1 S_95 1 S_60 1 S_244 1 S_201 1 S_95 1 S_60 1 S_244 1 S_170 1 S_60 1 S_244 1 S_127 1 S_60 1 S_244 1 S_189 1 S_244 1 S_60 1 S_244 1

Hip1R can be activated by clathrin OR CIN85 OR PIP2_45.\n \n

*Hip1R is recruited by clathrin light chains.{[]-p(168,171)} \n\n

*Hip1R is one of the CIN85 effectors. CIN85 clusters its effectors and recruits them.{[3]-p(3155)} \n\n

S_105 1 S_183 1

EGFR_Y891 (Tyr_891 site of EGFR) is phosphorylated (hence activated) by Src.\n\n

*Src phosphorylates EGFR on Y891 and Y920 (in vitro, []), as well as Y845 and Y1101 ([2],<cite>Jorrison</cite>-p.39,[3]). Y845 is phosphorylated by Src in vitro and vivo ([],<cite>Jorrison</cite>-p.39)\n<br>*Src is activated in response to growth factors such as PDGF, which induces PDFGR autophosphorylation {[6]-p(4)}\n<br>*Src kinase activity is required for phosphorylation of other tyrosine residues {[5]-p(2)}\n\n

S_244 1