Explaining gene ontology results by gage ?

Question

[Tania]

Hi all

A Very basic question as I am still trying this: If I used gage to get gene ontology, and this is a sample of what I get:

"","greater.p.geomean","greater.stat.mean","greater.p.val","greater.q.val","greater.set.size","greater.exp1","less.p.geomean","less.stat.mean","less.p.val","less.q.val","less.set.size","less.exp1","stats.stat.mean","stats.exp1"
"GO:0019226 transmission of nerve impulse",4.58857805313201e-17,8.54452633319693,4.58857805313206e-17,7.54490976367523e-14,329,4.58857805313199e-17,4.36162659873336e-41,-14.0993726059477,4.3616265987334e-41,1.18723476017523e-37,467,4.36162659873338e-41,8.54452633319693,8.54452633319693
"GO:0007268 synaptic transmission",5.54365155303099e-17,8.5494194949283,5.54365155303103e-17,7.54490976367523e-14,293,5.54365155303099e-17,9.32445527969831e-33,-12.3911725329985,9.32445527969837e-33,1.26905836356695e-29,431,9.32445527969828e-33,8.5494194949283,8.5494194949283

I am now confused of relating my top differential expressed genes with those GO ids. Like which of my top expressed genes are in which GO?

Answer 1

[Sharon]

Hi Tania

As far as I understand your question you can follow this link to use biomart to get genes in the GO term you have. So then you can fins which genes are in the GO you have,

How To Get Gene List From Each Gene Ontology Term?

[Tania]

Yes, that helps, thanks Sharon