Recommend Some Software/Package For Go Enrichment & Visualization

Question

[Casual]

Hi Everyone

I'm doing some transcriptome study,and got a bunch of transcript ID and corresponding GO IDs.Now I need statistical information for GO categories and want to visualized some results for my paper.

But these genes came from a rare species,most GO soft only support several limited species;and to make it worse, the ID list was too long for most web-based GO tools.

I already tried:DAVID,BiNGO,REViGO,GiTools,some Cytoscape plugins , All Failed.

Then I ran blast2go, which took such a long time. Although I got GO IDs, b2g doesn't take them as input, it only take blast results...

Could anybody give me a clue? Soft/package to take genes name/GO_IDs as input, and export some visualized results(even do categories count will be accepted) will be fine!

Thank you! and I'm glad to share any information~

[Sean Davis]

If you have transcript ids and GO ids for your entire transcriptome, you can use a fisher exact test to calculate the GO enrichment yourself. No special software is required. However, it is not clear what you actually have or do not have from your post.

[Davy]

Are you familiar with R and Bioconductor/BiomaRt?? What species are you working on?

[Casual]

I only can write Perl script,not familiar with R,But I hv good learning curve,I can learn R if necessary. It's kind of fish,similar with Takifugu rubripes.Now I have diff_exp gene/transcript ensemble IDs and sequence.After Interpro scan,also got GO IDs.

Answer 1

[Woa]

How about using GO::Termfinder? There are some threads on that in Biostar, here's an example

How To Use Go::Termfinder

[Woa]

along with

http://search.cpan.org/dist/GO-TermFinder/lib/GO/View.pm

Answer 2

[Obi Griffith]

Not sure if you will find a solution here. But a fairly comprehensive list of GO enrichment tools is listed on the Gene Ontology website.

[Adrian Pelin]

That's unfortunate, but The GO Tools Registry is no longer supported.