Gene list

[Patrick Western]

Hi UCSC,

I would like to search UCSC for a term (e.g. chromatin), have UCSC return a list of genes to me which contain this term anywhere in their descriptor/annotation and then download this to excel in a tab delimited form.

Is this possible? 

If so how do you do it?

If not, can you suggest a database in which I could do this?

Thank you for your help and time.

Regards,

Patrick

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Dr. Patrick Western
Group Leader, Germ Cell Development and Epigenetics,
Centre for Genetic Diseases,
MIMR-PHI Institute for Medical Research
PO Box 5418
27-31 Wright Street
Clayton, 3168

Tel:    +61 3 9902 4770
Fax:    +61 3 9594 7111
Email:  patrick...@monash.edu
Web page:    http://mimr-phi.org

[Luvina Guruvadoo]

Hello Patrick,

Thank you for your question. I recommend connecting to our public MySQL server and querying a table (refSeqSummary) to retrieve this information. If you are unfamiliar with our public MySQL server, you can read more about it here: http://genome.ucsc.edu/goldenPath/help/mysql.html. Once you are connected, you can use a query like:

mysql> select mrnaAcc, summary from refSeqSummary where summary like '%chromatin%';

This will provide you with a list of RefSeq mRNA accessions that contain the word "chromatin" in their description. Note, you can refer to the table schema for refSeqSummary to get a description of the table columns:
http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg19&hgta_doSchemaTable=refSeqSummary

Unfortunately, we do not provide tab delimited Excel downloads.

I hope this helps. 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.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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