Recommend Some Software/Package For Go Enrichment & Visualization
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~
• 4,973 views
•
link
updated
by
Obi Griffith
•
written
by
Casual •
•
written
by
Casual •
2 answers
How about using GO::Termfinder? There are some threads on that in Biostar, here's an example
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.
• 1 views
•
link
written
by
Obi Griffith
That's unfortunate, but The GO Tools Registry is no longer supported.
• 0 views
•
link
written
by
Adrian Pelin
Log in to answer this question.
More posts like this
-
After KEGG and GO analysis, how to make tables+phylogenetic trees
written by dimitrischat
-
Please help with REVIGO ANALYSIS
written by Bioinformatician_in_trouble •
-
Summarizing long list of GO terms
written by kevluv93
-
The way to get the all p-value of functionally annotated categories from DAVID?
written by kim •
-
Help For Usage Of Gene2Pathways(R Package For Kegg)
written by Casual •
-
How To Do Go Analysis Via Interpro Results?
written by Casual •
-
Protein Sequence Or Dna Sequence,Which Is Better For Go & Kegg Analysis?
written by Casual •
-
Cytoscape Plug-In For Retrieving Protein-Protein Interactions
written by Woa
-
About Fatigo+ Input Format
written by Dejian
-
Tools For Visualizing Overlap Between Go Terms
written by Michael Kuhn
Are you familiar with R and Bioconductor/BiomaRt?? What species are you working on?
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.
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.