I have a list id of GenBank accession like this:
NM_176890.1
BX101169.1
BM716958.1
NM_173652.1
AI808125.1
AA972198.1
AA235299.1
NM_003444.1
NM_012464.3
and I want to change it to entrez gene id, I tried DAVID, but failed, and BioMart, and others failed to. Can anyone advise some ways to me to finish this aim?
Thanks very much.
•
written
by
盛夏 •
2 answers
you can use clusterProfiler to convert gene IDs. see http://www.bioconductor.org/packages/3.2/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#bitr-biological-id-translator
> acc=read.table("acc.txt", header=F, stringsAsFactors=F)
> acc
V1
1 NM_176890.1
2 BX101169.1
3 BM716958.1
4 NM_173652.1
5 AI808125.1
6 AA972198.1
7 AA235299.1
8 NM_003444.1
9 NM_012464.3
> acc=gsub("\\.\\d", "", acc[,1])
> acc
[1] "NM_176890" "BX101169" "BM716958" "NM_173652" "AI808125" "AA972198"
[7] "AA235299" "NM_003444" "NM_012464"
> require(clusterProfiler)
> bitr(acc, fromType="ACCNUM", toType="ENTREZID", annoDb="org.Hs.eg.db")
ACCNUM ENTREZID
1 NM_176890 259296
4 NM_173652 285154
8 NM_003444 7710
9 NM_012464 7092
Warning message:
In bitr(acc, fromType = "ACCNUM", toType = "ENTREZID", annoDb = "org.Hs.eg.db") :
55.56% of input gene IDs are fail to map...
>
Some of the accession numbers your listed are not genes, and can't be mapped to entrez gene ID.
You can search them to verify, for example the AA235299.1 can be found in http://www.ncbi.nlm.nih.gov/nucest/1859736/.
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written
by
Guangchuang Yu
At present, when using annoDb it raises an error: Error in bitr(acc, fromType = "ACCNUM", toType = "ENTREZID", annoDb = "org.Hs.eg.db") : unused argument (annoDb = org.Hs.eg.db), therefore, it should be replaced with OrgDb = org.Hs.eg.db.
You can copy and paste these 9 accession numbers into NCBI Nucleotide and see that five are from the EST database. Of the four that are RefSeq accessions, two have been updated and two have had their records removed.
For ESTs, though it is a bit old-fashioned, you could look at UniGene, which maps ESTs to "clusters". Many of those clusters are, then, mapped to Entrez Gene IDs.
•
written
by
Sean Davis
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Note that most genbank accession numbers will not be directly linked to an Entrez Gene ID. That said, when you tried to do the conversions using online tools, what "failed"?
you mean like the genebank accession AA235299 is a EST, so it is not a gene, can't be mapped?
If you open these ID's in GenBank,the database itself contain link to entrez. For eg. open the site http://www.ncbi.nlm.nih.gov/genbank/. Paste your query like NM_176890 in the search text box and you will get the entire information (http://www.ncbi.nlm.nih.gov/nuccore/NM_176890 ). Here if you search Geneid it will highlight it like this "GeneID:259296"
but I need to change a lot of the GenBank accessions to entrez gen ids once a time. I cant query it one by one