Pathway Co-expression Illustrator

An AIP-workshop idea app. Given a gene locus, display the pathways it is involved in and give the co-expression of genes in that pathway and other genes co-expressed with them.

An AIP Science App created using Yeoman and the AIP science app generator.

Authors

• Dries Vaneechoulte
• Stephen Ficklin
• Umit Seren
• Sergio Contino
• Chuan Wang

GUI:

[ Locus Text Box ]
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[ Pathway Drop Down ]             |           HEAT MAP
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       Cytoscape Viewer           |
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     Genes Not in Pathway Co-Expressed with Pathway Genes


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Steps:

1. User provides single locus ID
2. Call pathway_by_locus service
   a. JSON is parsed to get the list of reactions
3. Select the first pathway
   a. For each reaction in the pathway
   i. Call the loci_of_reaction service and parse the JSON to retrieve the list of genes in the reaction
   ii. Call the atted_webservice to retrieve the co-expression information for each of genes in the list constructed in step 3.a.i
   b. Separate the gene list from step 3.a into two lists:
   i. Get co-expression data from genes in the pathway (will be used for heat map construction)
   ii. Get co-expression data from genes not in the pathway (will be used for table)
   c. Generate the Cytoscape JSON file for constructing the network view
4. Visualization
   a. Network View: pass the Cytoscape JSON to the Cytoscape.js plugin
   b. Heat Map:
   c. Co-expressed Genes Table: Construct the data table (perhaps using underscore library).
5. If user selects a different pathway, repeat step 3 but with the pathway frameid selected.