Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
0
0
Entering edit mode
4.7 years ago
O.rka ▴ 290

Is there a way to do something like gene ontology but with a list of HMM IDs in either PFAM or TIGRFAM format? I like how you can give DAVID a list of Uniprot identifiers, it may be interesting if you could actually look at enrichment of domains. Does this exist?

pfam tigrfam hmm gene ontology analysis • 1.4k views
ADD COMMENT
1
Entering edit mode

I don't think there's any ready-to-use tool for this but you could do it yourself. All you need is assign GO terms to HMM IDs, which can naively be done by transferring terms from the genes represented in each HMM.

ADD REPLY
1
Entering edit mode

You can use the gene names and test for the enrichment using DAVID or Enrichr. http://amp.pharm.mssm.edu/Enrichr/#stats

ADD REPLY

Login before adding your answer.

Traffic: 2426 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6