Gene Ontology terms and their GO IDs

[Chris Pam]

Hi,

Is there any way I can get a table for all Gene Ontology terms (eg.  acetyl-CoA biosynthetic process from pyruvate ) and their corresponding GO IDs (eg. GO:0006086) along with whether they are a parent or child node of whichever Gene Ontology/GO ID?

I would like to have them in a tabular format for visualization purposes.

Thanks

Chris

[Anthony Castanza]

Hi Chris,

 

You'll have to retrieve the GO Term hierarchy directly from the GO .obo files since we don't save that, but as to the term to name mappings, along with the formatted names we use in MSigDB, I'm attaching those here.

The attached file contains three columns, the first is the gene set name as formatted for MSigDB, the second column is the GO Term ID, and the third is the original name without any of our processing. This file is one that we generate internally during the gene set creation process so not all of the gene sets represented in it will necessarily have passed all thresholds for inclusion in MSigDB (some may have been screened out by a size thresholds) but there aren't going to be any GO gene sets included in MSigDB v7.4, C5:GO:BP, C5:GO:CC, or C5:GO:MF that aren't in this file.

 

Hope it helps,

 

Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Anthony Castanza]

Hi,

Sorry about that, Google Groups wasn't cooperating. Did the attachment come through this time?

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

[Pierre Laplante]

Hello,

Would you be so kind as to link the latest table for MSigDB GO term to GO ids?

Thank you very much.

Regards,

Pierre

[Anthony Castanza]

Hi Pierre,

We've moved to providing metadata about gene sets (such as the GO term IDs) in the json specification files available on the MSigDB downloads page.

For the GO data, you'd be interested in both the "exactSource" and "filteredBySimilarity" keys.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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