Cytoscape and gene network

Question

[bpatel]

Hello,

I have a list of 300 genes that have been determined to be differentially regulated after undergoing a differentiation process.

I'm fairly new in the bioinformatic filed but I was thinking of creating some sort of network showing the interactions these proteins may have with each other. Also, it would be cool to see if these proteins can be connected to one another via a pathway analysis.

I am open to any ideas also on how to further analyze my data.

[GouthamAtla]

You can use cytoscape and install different plug-ins that does functional enrichment analysis.

Have a look at Cytoscape Plug-In For Retrieving Protein-Protein Interactions

Answer 1

[Chirag Parsania]

I would suggest you to use cytoscap plugin BINGO followed by EnrichmentMap. These are very powerful plugins to create network of GO of differentially expressed genes.

~C.

Answer 2

[BioinfGuru]

The tutorial here is an easy step by step guide for GSEA using g:Profiler and passing the output to the EnrichmentMap plugin in Cytoscape. Great for keeping it basic.

I have to say though that you can do more manipulation and produce nicer maps with the iRegulon plugin in Cytoscape.

Also, have you considered just using STRING? It's another great tool, and pretty much a one stop shop for both pathway analysis and PPIs without having to install anything.