This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extracting chromosomal locations by ENTREZID

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
• 2,195 views • link
updated by Biostar Biostar • written by aln aln

3 answers

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
• 1 views • link
written by GenoMax GenoMax

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?

• 1 views • link
written by aln aln

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.

• 1 views • link
written by vkkodali_ncbi vkkodali_ncbi

Thanks a lot! Very convenient.

• 1 views • link
written by aln aln

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.

• 1 views • link
written by aln aln

Log in to answer this question.

More posts like this