A limited number of signalling pathways are involved in the specification of cell fate during the development of all animals. Several of these pathways were originally identified in Drosophila. To clarify their roles, and possible cross-talk, we have built a logical model for the nine key signalling pathways recurrently used in metazoan development. In each case, we considered the associated ligands, receptors, signal transducers, modulators, and transcription factors reported in the literature. Implemented using the logical modelling software GINsim, the resulting models qualitatively recapitulate the main characteristics of each pathway, in wild type as well as in various mutant situations (e.g. loss-of-function or gain-of-function). These models constitute pluggable modules that can be used to assemble comprehensive models of complex developmental processes. Moreover, these models of Drosophila pathways could serve as scaffolds for more complicated models of orthologous mammalian pathways. Comprehensive model annotations and GINsim files are provided for each of the nine considered pathways. Helikar Tomas thelika@unmc.edu University of Nebraska - Lincoln 2015-01-28T19:24:15Z 2016-01-22T07:08:46Z

necrotic (Nec) gene codes for the serine protease inhibitor (Serpin) SPN43Ac<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q6V6F8" 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);">Q6V6F8</a></div><div>Gene Name: nec</div><div>Gene ID:&nbsp;<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);">45908</span></div><div><br/></div><div><div><br/></div></div>

 2015-11-15T20:51:48Z

F-box protein Supernumary limbs (SLMB)<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q9VDE3" 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);">Q9VDE3</a><br/>Gene Name: slmb</div><div>Gene ID:&nbsp;<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);">42504</span><span style="font-size: 10pt;">&nbsp;</span></div>

 2015-11-15T20:51:48Z

dorsal-related immune responsive gene<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/P98149" 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(222, 239, 245);">P98149</a></div><div>Gene Name: Dif</div><div>Gene ID:&nbsp;<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);">35045</span></div>

 2015-11-15T20:51:48Z

a IkB\r\nfactor Cactus<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q03017" 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);">Q03017</a></div><div>Gene Name: cact</div><div>Gene ID:&nbsp;<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);">34969</span></div>

 2015-11-15T20:51:48Z

Drosophila Toll receptor family<div>Gene Name: TI</div><div>Gene ID:&nbsp;<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);">43222</span></div>

 2015-11-15T20:51:48Z

adaptor protein<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q7K105" 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(222, 239, 245);">Q7K105</a><br/><div>Gene Name:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/gene/35956" ref="ordinalpos=1&amp;ncbi_uid=35956&amp;link_uid=35956" 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);"><span class="highlight">Myd88</span></a></div><div>Gene ID:&nbsp;<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);">35956</span></div></div>

 2015-11-15T20:51:48Z

<span style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; background-color: rgb(255, 255, 255);">embryonic polarity protein</span><span class="highlight" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; background-color: rgb(255, 255, 255);">dorsal</span><div><span class="highlight" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; background-color: rgb(255, 255, 255);">UniProt ID:&nbsp;</span><a href="http://www.uniprot.org/uniprot/P15330" 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);">P15330</a></div><div><span class="highlight" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; background-color: rgb(255, 255, 255);">Gene Name: Dorsal</span></div><div><span class="highlight" style="font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 17.9998016357422px; background-color: rgb(255, 255, 255);">Gene ID:&nbsp;</span><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);">692440</span></div>

 2015-11-15T20:51:48Z

Protein spaetzle of&nbsp;&nbsp;the Toll pathway ligand<div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/P48607" 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(222, 239, 245);">P48607</a></div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">Gene Name: spz&nbsp;</div><div style="font-family: Arial, Verdana; font-size: 10pt; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;">Gene ID:&nbsp;<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);">43256</span></div>

 2015-11-15T20:51:48Z

Tube adaptor protein<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/P22812" 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);">P22812</a></div><div>Gene Name: tub</div><div>Gene ID:&nbsp;<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);">40554</span></div>

 2015-11-15T20:51:48Z

Pelle is a serine, threonine kinase.<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q05652" 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);">Q05652</a></div><div>Gene Name: pll</div><div>Gene ID:&nbsp;<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);">43283</span></div>

 2015-11-15T20:51:48Z

Target nodes from the paper [1]

 2015-11-15T20:51:48Z

Cactus inhibits Dif [1, 2, 3].

DIF was identified as a dorsal-related immune responsive gene that does not\r\nparticipate in dorsal ventral patterning. Instead, it mediates an immune\r\nresponse in Drosophila larvae and interacts with Cactus. [1, 2, 3]&nbsp;

 S_2 1

Pelle and Slmb inhibit Cactus [1, 2, 3].

Slmb inhibits Cactus [1]

To be\r\ndegraded, Cactus is phosphorylated by Pelle. [1, 2, 3]

 S_10 1 S_6 1

<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);">Spz activates Toll [1]</span>

Spz activates Toll [1]

 S_8 1

Toll activates MyD88 [1, 2, 3, 4].

The TIR interleukin-1 receptor domain of Toll binds to the TIR domain of\r\nMyD88, however, binding occurs only when the receptor is active. [1, 2, 3, 4]

 S_3 1

Cactus inhibits Dorsal [1]

<span style="font-size: 13.3333330154419px;">Cactus inhibits Dorsal [1]</span>

 S_2 1

<span style="font-size: 13.3333330154419px;">Nec inhibits Spz [1]</span>

Nec inhibits Spz [1]

 S_4 1

<span style="font-size: 13.3333330154419px;">MyD88 positively regulates Tube [1]</span>

MyD88 positively regulates Tube [1]

 S_5 1

Tube activates Pelle [1, 2, 3].

Pelle has been shown to auto-phosphorylate himself and to phosphorylate\r\nToll and Tube. [1, 2, 3]

 S_9 1

<span style="font-size: 13.3333330154419px;">Dif activates the Target nodes [1].&nbsp;</span><span style="font-size: 13.3333330154419px;">Dorsal activates the Target nodes [1]</span>

<span style="font-size: 13.3333330154419px;">Dorsal activates the Target nodes [1]</span>

Dif activates the Target nodes [1]

 S_1 1 S_7 1