Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl website, how to deal with it?
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?
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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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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?I will update this post as soon as there is new progress.
Any update on this bug?
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