Question: Go Term enrichment
0
gravatar for Arsalan
3.6 years ago by
Arsalan10
Arsalan10 wrote:

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

go cluster • 1.1k views
ADD COMMENTlink modified 3.6 years ago by tallulandrews30 • written 3.6 years ago by Arsalan10
1

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

ADD REPLYlink written 3.6 years ago by Jean-Karim Heriche19k
3
gravatar for tallulandrews
3.6 years ago by
United Kingdom
tallulandrews30 wrote:

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

 

http://revigo.irb.hr/

ADD COMMENTlink written 3.6 years ago by tallulandrews30
1

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!

ADD REPLYlink written 3.6 years ago by jerry10

Many thanks

ADD REPLYlink written 3.6 years ago by Arsalan10
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