Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl website, how to deal with it?
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3.7 years ago
Makplus T ▴ 70

Hello, as a newbie, I do get some troubles in converting ensembl ID to gene SYMBOL.

For example, when I convert the "ENSG00000158164" to SYMBOL in the R library "org.Hs.eg.db", it has 2 symbol names. This is my code and output:

> select(org.Hs.eg.db, keys="ENSG00000158164",columns=c("CHR","SYMBOL","GENENAME"), keytype="ENSEMBL")
'select()' returned 1:many mapping between keys and columns
          ENSEMBL         CHR       SYMBOL          GENENAME
1 ENSG00000158164    X        TMSB15A         thymosin beta 15a
2 ENSG00000158164    X        TMSB15B         thymosin beta 15B

But actually the ensembl ID of TMSB15B is ENSG00000158427;

> select(org.Hs.eg.db, keys="ENSG00000158427",columns=c("CHR","SYMBOL","GENENAME"), keytype="ENSEMBL")
'select()' returned 1:1 mapping between keys and columns
          ENSEMBL.         CHR       SYMBOL          GENENAME
1 ENSG00000158427      X        TMSB15B       thymosin beta 15B

Could someone suggest me how to deal with it?

org.Hs.eg.db ensembl gene symbol • 4.1k views
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This looks like the results of a bug in the script that was used to make org.Hs.eg.db, can you report it to the package maintainer?

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I will update this post as soon as there is new progress.

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Any update on this bug?

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Hello These are two separate genes in Ensembl version 99: TMSB15A: https://www.ensembl.org/Multi/Search/Results?q=ENSG00000158164 TMSB15B: https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000158427 I suggest to check which version this R library uses. Astrid Ensembl helpdesk

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20 months ago

Because "TMSB15A" is old name of TMSB15B, both two results are right. You can see detail information in the follow link: https://asia.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000158427;r=X:103918896-103966712

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