Kegg Pathway Analysis

Question

[vj]

Hello,

I have multiple sets of genes (as gene_symbol s) and I need to calculate overrepresented KEGG pathways in each of these gene sets. Is there any stand-alone software that can do this?

Thank you.

[Manu Prestat]

You have sets of gene IDs only? Or you have also their "abundance" or their expression? To sum-up, what do you call an overrepresentation?

[vj]

I have their abundances too. Do you think I can use them too in the analysis. What I mean by "over-represented KEGG terms" is similar to identifying enriched GO terms - for example. performing hypergeometric test as done by cytoscape plugins like BiNGO.

I hope this answers your question.

Thanks.

Answer 1

[Heather Vincent]

You can use DAVID (http://david.abcc.ncifcrf.gov/) for various functional classifications. I think that most other tools do expect expression data.

[vj]

I do use DAVID however I have many sets of genes and I am having a hard time using DAVID multiple times. Do you know of a way to automate it or may be a stand-alone tool that is similar to DAVID?

Thanks for the suggestion.

[EagleEye]

GeneSCF... Command line based and supports batch analysis.