Go Term enrichment

Question

[Phismil]

Hello , I am a new comer in the field of functional genomics and apologize for easy question in advance. I have a series of sequences that I have assigned GO term in Blast To Go. I am wondering if there is any way to import these GO terms in to a program and then cluster them based on their biological functionality. I checked David but it seems it need Gene IDs rather than Go terms.

Many thanks in advance

[Jean-Karim Heriche]

Do you want to cluster GO terms themselves or actually cluster your sequences using functional similarity indicated by associated GO terms ?

Answer 1

[tallulandrews]

ReviGO works straight from GO terms, you provide weights for each term (typically a p-value but could be sequence count in this case)

[jerry]

ReviGO looks like it will cluster your GO terms by similar process, which I think is what you want to do. As a follow-up, if you have some basic programming knowledge, you could then write some scripts to parse your Blast2GO output file and get the list of genes associated with a specific GO term cluster you are interested in. I am assuming this is ultimately what you want to do.

Hope that helps!

[Phismil]

Many thanks