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is there anyway to investigate a specific pathway

Hello,

I would like to know if there is any way that I check for a specific pathway using my gene list ?

I have a list of genes which are unregulated and I only want to check if a specific pathway is activated or not

Thanks

r pathway analysis python gene
• 2,710 views • link
updated by Ron Ron • written by Learner Learner

@reza.jabal DAVID is not the way to go, but thanks

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written by Learner Learner

2 answers

Gene Set Clustering based on Functional annotation (GeneSCF)

try GeneSCF, simple command line tool accepts gene list and perform enrichment analysis in real-time (directly extract information from selected database). You can also choose between different database GO, KEGG, REACTOME.

http://genescf.kandurilab.org

• 1 views • link
written by EagleEye EagleEye

Use GSEA http://software.broadinstitute.org/gsea/index.jsp I am assuming the pathway and the list of genes is same. It will give enrichment results if your pathway is upregulated or down regulated with p-values. Also you can search for your own pathways,curate your own pathways to look for enrichments in your data.

• 0 views • link
written by Ron Ron

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