Question

Converting GeneBank Access number into Entrez gene IDs

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Sanches • 0

@sanches-13853

Last seen 6.6 years ago

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

Annotation • 914 views

ADD COMMENT • link updated 7.1 years ago by James W. MacDonald 67k • written 7.1 years ago by Sanches • 0

score 1 · Answer 1 · 2017-09-06

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 hours ago

United States

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 COMMENT • link 7.1 years ago James W. MacDonald 67k

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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 REPLY • link 7.1 years ago Sanches • 0