DAVID For genes list greater than 3000

Question

[damiano.bassani]

Hi!

I need to do a Go analysis. Until now I used David. Unfortunately, the option " Functional annotation clustering " allows to load lists of genes up to a total of 3000 items. But now I have to carry out an analysis on a list bigger than 3000 items and I don't know how to do it.

Any suggestion?

Thank you very much! Bye

[mikhail.shugay]

Just a suggestion: 1) move to other GO annotation software, DAVID is a bit outdated in terms of GO database version 2) When doing enrichment analysis, lists with more than ~150 genes are almost guaranteed to produce some highly-enriched clusters/GO categories. So you should try more stringent criteria for gene list selection, going down from 3000+ decreases the risk of false-positives.

Answer 1

[EagleEye]

You can use this command line tool which has updated dataset than DAVID. It works for Human and it is linux based tool.

Gene Set Clustering based on Functional annotation (GeneSCF)