Fetch Phenotypes from Orthologues and GO terms for a NonModel organism Gene Set
1
0
Entering edit mode
6.5 years ago
FatihSarigol ▴ 250

Hi all,

What I am trying to do is simply a way to get a table which would connect my genes to phenotypes,

As an example when I search ENSACAG00000010391 on ensembl.org, I can find them manually when I click Phenotypes on left, hits go like this:

decreased circulating potassium level MGI Mouse (Mus musculus) ENSMUSG00000053522 Lgals7 increased circulating glycerol level ... ...

And GO terms (only molecular function) is available for this:

GO:0030246 carbohydrate binding

I tried Biomart but couldn't find a way.

Is there a way to extract a table for several genes at once, one line would be like this?

ENSACAG00000010391  (Orthologous Phenotypes Column) decreased circulating potassium level, increased circulating glycerol level (GO:Molecular Function column) carbohydrate binding

Thanks!

ensembl biomart gene ontology • 1.3k views
ADD COMMENT
3
Entering edit mode
6.5 years ago
Emily 23k

You can do this by combining species datasets, see this help page. Use your non-model species as your first database then filter by IDs. Use the model species as your second dataset and get phenotypes and GO terms as attributes.

ADD COMMENT

Login before adding your answer.

Traffic: 1636 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6