Search
Question: how to retrieve gene id from topGO results
0
gravatar for ycding
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
ADD COMMENTlink 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. 

ADD REPLYlink written 12 days ago by shepherl ♦♦ 890
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 410 users visited in the last hour