Disease Causing Genes

[Victoria Stinnett]

Hello,

I was wondering if it was possible to export a list of all genes associated with a known phenotype or disease from your website. These would be the "green" OMIM RefSeq genes we see in your broswer.  We would like to export the list to use with our analysis software so that it matches with UCSC. 

Any help you can provide is appreciated. ​

Thank you,

Victoria Stinnett

Sr. Cytogenetics Technologist

Johns Hopkins Hospital

Baltimore, Maryland

[Christopher Lee]

Hi Victoria,

Thank you for your question about exporting a list of genes associated
with a certain OMIM phenotype. Due to agreements with OMIM, we
currently do not offer genome-wide downloads of any data associated
with OMIM. If you would like to download this data you should contact
OMIM here:
http://omim.org/downloads/

After downloading the data from OMIM directly, you can post process
the data and obtain all genes associated with a specific phenotype. If
you would like to reconstruct the data shown at the UCSC Genome
Browser, you can follow the steps from the Methods section of the
track description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=omimGene2

OMIM provides the data in UCSC format so it should be straightforward
enough to get the data you are looking for.

That said, if you would like to obtain all genes associated with a
particular phenotype on a chromosome by chromosome basis, this is
possible via the Table Browser:

1. Navigate to the Table Browser: https://genome.ucsc.edu/cgi-bin/hgTables.
2. Select your assembly of interest, for this example I will be using
Human Feb. 2009 (GRCh37/hg19).
3. Make the following selections:
- group: Phenotype and Literature
- region: Select position and enter chr1 (repeat for all chromosomes)
- track: OMIM Genes
- table: omimGene2
4. Click the "create" button next to "filter".
5. Scroll down to the "Linked Tables" section and check the box next
to omimPhenotype. Scroll down all the way to the bottom of the page
and click "allow filtering using fields in checked tables".
6. In the "hg19.omimPhenotype based filters" free-form query box,
enter the ID of the phenotype you are interested in in the phenotypeId
box (in this example I will use 105400 for Amyotrophic lateral
sclerosis 1) and change "ignored" to "=". In the phenotypeMapKey box,
enter "3" for dark green genes and again change "ignored" to "=".
7. Click "submit".
8. Change the "output format" dropdown to "selected fields from
primary and related tables".
9. Click "get output".
10. On the resulting page, in the "Linked Tables" section, check the
box next to omimPhenotype and click "allow selection from checked
tables". Select the fields you are interested in from the omimGene2
table, and select description from the omimPhenotype table.
11. Click "get output".

The result will be output like the following, depending on the fields
selected in Step 10:

chr21 33031934 33041243 147450 Amyotrophic lateral sclerosis 1

Again, it would be preferable to contact OMIM to obtain this data
instead of querying the Table Browser by chromosome.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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