4
$\begingroup$

I am looking for a place where I can download a full gene list of human genome. Either by HGNC symbol or ensemble ID as long as it is usable on the consensusPathdatabase. Up until this point I have only found fasta files which include a bit too much information and unfortunately not in the format I would like. I am not in the biology field myself so if I am asking for something unreasonable call me out on it!

Reason for this is I am trying to stress test an application that uses the output tabular forms from the gene set analysis tool on consensusPathbase. The stress test on the entire human genome seemed to be the best option as a bigger data set than that will probably not occur.

Thanks in advance

Improve this question
$\endgroup$

1 Answer 1

Reset to default
5
$\begingroup$

The database you are looking for is ensembl [Yates (2016)].

Go here and chose Customise your download. There you can select a dataset (e.g. genes and then specify human genes - currently uses build GRCh38; you can also go the same way here to do the same for hg19/GRCh37).

After chosing your dataset, you can click on Attributes to specify what to include in your download (HGNC symbols, IDs, regions, GO terms, and a ton of other stuff), click on Filters to apply filters to your choices (only genes from a chromosome, region, and a ton of other stuff).

Then click Results and download your selection in a format of choice.

(Hint: click Count first and use it as a a sanity check to see if the number of selected genes fits your expectation.)

Improve this answer
$\endgroup$
1
  • 1
    $\begingroup$ This is exactly what I was looking for. Thank you very much for the help! $\endgroup$
    – Marciano
    May 23, 2017 at 15:20

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .