Question: Extracting chromosomal locations by ENTREZID
1
gravatar for aln
10 weeks ago by
aln260
Ukraine
aln260 wrote:

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 • 196 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by aln260
4
gravatar for genomax
10 weeks ago by
genomax62k
United States
genomax62k wrote:

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
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by genomax62k

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?

ADD REPLYlink written 10 weeks ago by aln260
4
gravatar for vkkodali
10 weeks ago by
vkkodali950
United States
vkkodali950 wrote:

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.

ADD COMMENTlink written 10 weeks ago by vkkodali950

Thanks a lot! Very convenient.

ADD REPLYlink written 10 weeks ago by aln260
0
gravatar for aln
10 weeks ago by
aln260
Ukraine
aln260 wrote:

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.

ADD COMMENTlink written 10 weeks ago by aln260
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