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Question: Converting GeneBank Access number into Entrez gene IDs
1
gravatar for Sanches
11 weeks ago by
Sanches0
Sanches0 wrote:

Hi there, 

I have been running two-color microarray data from Agilent and  I would like an advice to convert GeneBank Access number into  Entrez gene IDs?

Cheers

 

ADD COMMENTlink modified 11 weeks ago by James W. MacDonald45k • written 11 weeks ago by Sanches0
1
gravatar for James W. MacDonald
11 weeks ago by
United States
James W. MacDonald45k wrote:

How you do that depends on the species you are working with. Let's assume you have human data.

> library(org.Hs.eg.db)
> select(org.Hs.eg.db, "U43746", "ENTREZID","ACCNUM")
'select()' returned 1:1 mapping between keys and columns
  ACCNUM ENTREZID
1 U43746      675

There are many orgDb packages that you can install, and even more that you can get on the AnnotationHub. I would recommend reading the vignettes for the AnnotationDbi and AnnotationHub packages to get yourself acquainted.

ADD COMMENTlink written 11 weeks ago by James W. MacDonald45k

Thanks for your tip, James. I will check it.

I have just tried it. I was not able to do that.

I would like to convert SystematicName(GeneBank Access Number) into Entrez gene IDs. Could anyone help me?

    > head(DE21)
          Row  Col    ControlType     ProbeName       SystematicName           logFC   AveExpr     t        P.Value     adj.P.Val    B
403     3       75            0              A_23_P95930      NM_003483                 5.57         8.30      21.7     2.33e-06    0.0461 4.60
49164 300 128           0              A_23_P92042      NM_002222                -3.30         7.42      -20.2    3.44e-06    0.0461 4.41
6279   39     47            0              A_33_P3369761  NM_001161779           5.86        11.06      20.0    3.62e-06    0.0461 4.38

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Sanches0
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