Fetch Phenotypes from Orthologues and GO terms for a NonModel organism Gene Set
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


ensembl biomart gene ontology • 1.3k views
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.


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