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Question: how to retrieve gene id from topGO results
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12 days ago by
ycding10
United States
ycding10 wrote:

HI edgeR users,

I identified differential expressed genes (DEGs) using the edgeR and then did gene ontology analysis for top 100 DEGs. I got the following results. the first GO term is the immune system process, there are 42 of my top 100 genes are in this immune related process.  how do I retrieve the list of those 42 entrez id since my input vector is 100 entriez gene ID?

Thank you,

Ding

> go <- goana(ids\$ENTREZID, species="Hs")
> topGO(go, n=5)
Term Ont    N DE
GO:0002376                  immune system process  BP 3038 42
GO:0006955                        immune response  BP 2176 34
GO:0002252                immune effector process  BP 1204 25
GO:0071357 cellular response to type I interferon  BP   89  9
GO:0060337    type I interferon signaling pathway  BP   89  9
written 12 days ago by ycding10

You could look at the mapping objects in org.Hs.eg.db The org.Hs.egGO might be a useful.