Question: How To Get Gene List From Each Gene Ontology Term?
3
gravatar for Omid
5.9 years ago by
Omid540
Netherlands
Omid540 wrote:

Hi,

I have a long list of Gene Ontology(GO) term like below and I would like to put this list in a on-line free available webpage and then receive the genes which categorize in each GO term ID.

Thanks

GO:0007099 GO:0043516 GO:0045665 GO:0051651 GO:0007017 GO:0051235 GO:0007059 GO:0046777 GO:0051640 GO:0000278 GO:0051301 GO:0048285 GO:0007049

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ADD COMMENTlink modified 5.9 years ago by Emily_Ensembl18k • written 5.9 years ago by Omid540
3
gravatar for Emily_Ensembl
5.9 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

You can do this in BioMart on Ensembl.

There's a help video on using BioMart here:

<iframe></iframe>

The tool is here: http://www.ensembl.org/biomart/martview/c7904f8b46d31846e072964b3ca0955a

You can just filter by GO accessions, then get gene names as attributes.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Emily_Ensembl18k

I really appreciate

ADD REPLYlink written 5.9 years ago by Omid540

Dear Emily,

I think there is some discordance. For example GO:0044702 is: single organism reproductive process

But when I put it in Biomart I got GO:0001541 which is:ovarian follicle development

Do you know what the resoan? is and how can I solve the problem?

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Omid540
1

I assume that you're filtering by GO:0044702, then selecting GO term accession as an attribute?

What's happening here is that the GO terms that you get out of BioMart are the most specific ones available. GO terms are hierarchical, so GO:0044702 is a very general term, and GO:0001541 is a more specific term which is a subset of GO:0044702. So everything with the GO term GO:0001541 will pass the filter for GO:0044702, but only GO:0001541, or other more specific GO terms, such as GO:0001554 and GO:0007276, will be displayed.

ADD REPLYlink written 5.9 years ago by Emily_Ensembl18k

Thanks,

But for my calculation I need just GO:0044702 and the genes which located in this GO term not the others.

ADD REPLYlink written 5.9 years ago by Omid540
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