Any tools out there for Interproscan enrichment analysis?

Question

[Biogeek]

Guys,

I've looked across the net and I'm failing to find a suitable tool or script to do some IPR term enrichment analysis. I've already done GO terms via GOATOOLS, but I'm struggling to find suitable resources for IPR enrichment. Any ideas?

Thanks.

Answer 1

[Jean-Karim Heriche]

If you're looking for protein domain enrichment, you can simply count occurrences of each domain in your two lists of genes and do a Fisher's exact test.

[Biogeek]

Hi Jean, I'm aware of this process; however, given that I want to test around 800 IPR terms in my foreground set vs my background, how can i deal with such large contingency tables? Do you know a straight forward program or method I can follow? Thanks.

[Jean-Karim Heriche]

Fisher's exact test can be applied to a m x n contingency table. If your expected cell counts are large enough (i.e. >5), you can also use the chi-squared test. However, testing on the whole table is only going to tell you whether there is any statistically significant difference but won't tell you where this difference is. If you care about finding which domain is over/under-represented then you have to test each domain individually and correct for multiple testing.