Counting genes based on GO terms

Question

[kevluv93]

Lets say I have a list of gene IDs. I want to assign them GO terms and then make a chart that shows how many times a GO term showed up on the list of genes. Like a bar graph with GO terms on one axis. However, I cannot use blast2go because I only have a list of genes and no sequences, and blast2go basic requires you to input sequences to work. I do not want to buy blast2go pro either. I've had limited success with PANTHER, however I want to be able to adjust the "levels" of GO terms that I can use. So by that I mean I might want to have the GO terms specific enough where "mitotic nuclear division" may be a GO term as opposed to "cell cycle".

Can anyone suggest a good program that can do this? Thanks!

Edit: I am analyzing a non-model organism. Most of these web-based programs that have pre-formatted gene IDs for a specific species will not work on my dataset.

[zizigolu]

REVIGO can summarize all of gene IDs belong to a GO term, and in the result page of AGrigo analysis with affy IDs as entry, you can see how many IDs mapped to a GO id...you know i like to help too much even my answer is irrelevant...

[zizigolu]

http://www.broadinstitute.org/gsea/msigdb/geneset_page.jsp?geneSetName=CELL_CYCLE_PHASE has something about cell cycle, and this post and this one

[zizigolu]

i think in http://wiki.c2b2.columbia.edu/workbench/index.php/Gene_Ontology_Viewer, gene list section you can find some information

Answer 1

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF) And more on GO enrichment analysis using a Text file with all the genes and GO ids associated for a non model organism

Answer 2

[Steven Lakin]

Does this webtool get you at least part way? http://go.princeton.edu/cgi-bin/GOTermMapper They also have a GO Finder tool that might be of interest.

Answer 3

[Na Sed]

Have you seen GOSemSim package?

I think you can use its procedures to get what you want.