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Extracting chromosomal locations by ENTREZID
1
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20 months ago
aln • 290
@aln9248

I feel like I'm missing smth very trivial, but how to automatically extract the most complete information on genes chromosomal locations using ENTREZID (preferably in R). I specifically have problems with uncharacterized loci (but sometimes with some genes also). When I use some typical approaches in R I get NA for those loci (e.g. by extracting info from org.Hs.eg.db, v. 3.7.0). For example, this gene - https://www.ncbi.nlm.nih.gov/gene/?term=LOC105370787.

R gene • 312 views
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2.1 years ago
genomax 68k
@genomax

Not a solution in R but you can use NCBI unix utils to get this information.

$ efetch -db gene -id LOC105370787 

1. LOC105370787
uncharacterized LOC105370787 [Homo sapiens (human)]
Chromosome: 15; Location: 15q15.1
Annotation: Chromosome 15 NC_000015.10 (40075943..40083225, complement)
ID: 105370787
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Thx, at least it sounds much more automatic than googling manually:) But why this info is not in the org.db package, while identifiers for the genes in question are totally present? Because it has not been updated yet?

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2.1 years ago
vkkodali ♦ 1.1k
@vkkodali30494

If you want a tab-delimited output that can be easily imported into R, you can use xtract, another tool from the Entrez Direct package as follows:

esearch -db gene -q LOC105370787 | esummary | xtract -pattern DocumentSummary -element Id,Name -group GenomicInfoType -element ChrAccVer,ChrStart,ChrStop
105370787       LOC105370787    NC_000015.10    40083224        40075942

There's additional information in the XML output of esummary that may be of interest to you.

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Thanks a lot! Very convenient.

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2.1 years ago
aln • 290
@aln9248

I've also found that if one needs only chromosome and band it is possible to extract this info from the NCBI Homo_sapiens.gene_info.gz file, which has tab separated format.

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