Question: Cytoscape and gene network
3
gravatar for bpatel
2.3 years ago by
bpatel30
bpatel30 wrote:

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.

cytoscape gene ontology • 996 views
ADD COMMENTlink modified 2.3 years ago by YaGalbi1.4k • written 2.3 years ago by bpatel30

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

ADD REPLYlink written 2.3 years ago by geek_y9.3k
1
gravatar for Chirag Parsania
2.3 years ago by
Chirag Parsania1.4k
University of Macau
Chirag Parsania1.4k wrote:

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.

ADD COMMENTlink written 2.3 years ago by Chirag Parsania1.4k
1
gravatar for YaGalbi
2.3 years ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

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.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by YaGalbi1.4k
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