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Pathway Enrichment & Genes Shared Between The Pathways

Hi!

This is extension of the thread related to pathway enrichment tools discussed previously and quite extensively here on Biostars.

I have little complicated question:

Imagine you have a list of genes (more than 1000) and you want to know the pathways that are enriched by them (with p value <0.05) and also the number of genes shared between these pathways.

Any ideas to do this in less time consuming & efficient manner?

Thank you

enrichment r
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updated by lkmklsmn lkmklsmn • written by Dataminer Dataminer

Maybe you could link the previous thread here so people know what you are talking about ;-)

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written by Michael Schubert Michael Schubert

7 answers

I like very much the list of tools posted here:

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Hi, we recently developed FIDEA a tool thought to facilitate the enrichment analysis. You can find it at http://www.biocomputing.it/fidea If you think that it is useful for your purpose and/or you need help let me know.

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updated by Giovanni M Dall'Olio Giovanni M Dall'Olio • written by luigra • luigra

Hi, have you used the modular enrichment analysis of DAVID?

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written by enunvillafer • enunvillafer

DAVID and webgastalt would be your choice

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written by ewre ewre

You can also see pathway enrichment at the various InterMine sites, e.g for human genes you can upload a list at metabolicMine: http://metabolicmine.org/beta/bag.do, for fly use FlyMine: http://www.flymine.org/query/bag.do.

I think you can also do enrichment calculations via the API.

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written by Richard Smith Richard Smith

I now use this: Lynx developed at the Computation Institute at the University of Chicago. It includes a network based prioritization algorithm here. You can batch upload big lists of genes. I haven't done 1000 yet, but I bet you probably could. Plus, they have a web service.

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written by Alex Paciorkowski Alex Paciorkowski

Good one :) Thank you

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written by Dataminer Dataminer

I usually download the pathway annotation system and then convert it into an adjacency matrix. Using Fisher's Exact test you can then easily determine significance of gene set overlaps!

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written by lkmklsmn lkmklsmn

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