Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
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?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
written by O.rka
-
pfam tigrfam mixed database
written by Moses
-
Mapping from TIGRFAM to PFAM
written by Selenocysteine
-
Most up-to-date Gene Ontology [GO] analysis?
written by O.rka
-
Gene ontology type analysis for pfam/tigrfams ?
written by jolespin
-
Mapping Uniprot Proteome identifiers to a taxonomic tree
written by Patrick •
-
Gene Ontology Enrichment
written by kevluv93
-
Identification Of Protein Complexes In A List Of Proteins
written by Pappu
-
Riken Identifiers: Conversion To Fastas
written by Anima Mundi
-
Biomart Retrieving One To Many Annotations
written by Jeremy •
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.
You can use the gene names and test for the enrichment using DAVID or Enrichr. http://amp.pharm.mssm.edu/Enrichr/#stats