Question: How To Download The Entire Human Gene List With Their Chromosomal Location
3
gravatar for arulthasan83cyr
4.8 years ago by
arulthasan83cyr30 wrote:

Dear Friends, I want to download the entire human gene list with the information about their chromosomal location, i.e. that specific gene is present in which chromosome and which arm (p or q). Is there any specific databases to give such an information, please guide me. Thanking in advance for the replies.

genes • 13k views
ADD COMMENTlink modified 4.8 years ago by PoGibas4.7k • written 4.8 years ago by arulthasan83cyr30
6
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

Just use Biomart. Using the Ensembl annotation, you can get a list of Ensembl IDs, the associated gene names, chromosome, position, and band (such as p22.1). You can also filter the results for the exact type of gene (known, novel, etc.) you want.

Edit: FYI, if you just want the actual coordinates instead, just download a GTF file or follow one of the other answers.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Devon Ryan81k
2
gravatar for PoGibas
4.8 years ago by
PoGibas4.7k
Vilnius
PoGibas4.7k wrote:

My suggestion would be Gencode genes (version 18 - 57445 human genes).
Annotation is in base pairs (much more accurate than chromosome arms).
All you have to do is:

  curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/release_18/gencode.v18.annotation.gtf.gz" | 
     gunzip -c > Human_genes.gtf

It's in GTF format.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by PoGibas4.7k

mkosinski@mkosinski-E540:~$ curl -s "ftp://ftp.sanger.ac.uk/pub/gencode/release_18/gencode.v18.annotation.gtf.gz" | gunzip -c > Human_genes.gtf

gzip: stdin: unexpected end of file

ADD REPLYlink written 19 months ago by MarcinKosinski10

The half life of a link in bioinformatics is just a few months. It looks like this has moved to "ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_18/gencode.v18.annotation.gtf.gz". You may as well check for a newer release. As of March 28 2017, it seems that release 26 is the most up to date.

ADD REPLYlink written 15 months ago by gui11aume10
1
gravatar for André Rendeiro
4.8 years ago by
Vienna, Austria
André Rendeiro50 wrote:

There are several places which provide databases on human gene annotation for download.

Try the Ensembl databases (http://www.ensembl.org/downloads.html) or data from the UCSC genome browser (http://hgdownload.soe.ucsc.edu/downloads.html#human) for example.

ADD COMMENTlink written 4.8 years ago by André Rendeiro50
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