Question: Extracting chromosomal locations by ENTREZID
1
gravatar for aln
10 days ago by
aln170
Ukraine
aln170 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 • 127 views
ADD COMMENTlink modified 9 days ago • written 10 days ago by aln170
4
gravatar for genomax
10 days ago by
genomax59k
United States
genomax59k 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 days ago • written 10 days ago by genomax59k

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 days ago by aln170
4
gravatar for vkkodali
10 days ago by
vkkodali660
United States
vkkodali660 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 days ago by vkkodali660

Thanks a lot! Very convenient.

ADD REPLYlink written 10 days ago by aln170
0
gravatar for aln
9 days ago by
aln170
Ukraine
aln170 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 9 days ago by aln170
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