tools for visulization of GO term's relationships?

[zinky]

hi
there are several GO terms generated by GO enrichment analysis on my hand, according to the p-value of each GO term ,we can easily infer which GO are most signifcantly enriched among whole term list . now i wanna have a look at relationships between those GO terms .
any tool or method recommended?

[JackieBadger]

BLAST2GO can create GO pathway maps via its pipeline. Im sure it could do the same with your data providing correct format of input spreadsheet.

[zinky]

yep, I know this, i used to employ blast2go to annotation my sequences ,it was a little time comsuming. anyway i will try it again .
thanks for your kind reply.

[fengqi]

I have used once GOrilla, you may want to try it.

http://cbl-gorilla.cs.technion.ac.il/

[zinky]

I have used once GOrilla, you may want to try it.

http://cbl-gorilla.cs.technion.ac.il/

thanks !
this seems a useful tool for me, but there is still a problem.GOrilla can do GO enrichment analysis with a list of genes we supplied and we can set our own genelist as backgound data, this seems good. I read the paper and found that it employs HGT as analysis method,what if i do analysis by other way? suppose i just want to visulize GO terms generated by myself, dose it works?

[Thomas Doktor]

GOrilla links to REVIGO which I think will do what you are looking for:

http://revigo.irb.hr/

[zinky]

thank you all, i think i got what i want exactly!!!

[Hel]

Hey! How did you get your list of GO terms and p-values? I run blast2go, but I only got a list of GO terms, lacking the e-values… Thanks in advance!

[zinky]

as i know, the blast2go output dose not contains P value of each GO term. the Pvalue mentioned above is calculated by extra test such as Fisher's exact test or hypergeometric test . you may write a script to do this .

[Hel]

Ok, thanks!