GO specific terms

Question: GO specific terms

2.5 years ago by

Canada

ajmaninisha • 30 wrote:

Hi All,

I have ensemble ids and i want to find the specific terms associated with it, I used biomart and it gave me the results related to biological process, cellular component and molecular function. But i want to specifically look for the term reproduction . Is there a way out to categorize the GO terms and search for specific terms.

i am doing my research on a non-model organism "lamprey". So most of the software programs doesnt have lamprey in their organism list .

Kindly advise

Nisha

gene id biomart go • 529 views

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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by ajmaninisha • 30

2.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, all three of these categories will be in the global list. You could filter the terms from Biomart with the tool Select first, then perform a Column Join on the common identifiers (Ensembl IDs) with that result. Just be aware that there is nesting within GO categories and you might miss some relevant content this way.

I was going to suggest these sites as an alternative since the searches are more flexible, but I also did not find much or any annotation for your target species. Somewhat odd that Biomart contains the content and others do not.

http://geneontology.org/ - Just a few hits
http://amigo.geneontology.org/amigo/term/NCBITaxon:7745 - None
http://genome.ucsc.edu - Has a browser with Gene tracks, but no track for Gene Ontology (that I could locate, in the browser or downloads area)

I hope the filter tools will be enough help! Jen, Galaxy team

ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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