Get chromosome location for a groupe of gene

[Serge Mcgraw]

Hi,
I'm wondering if it's possible to get the chromosome location for a groupe of genes. I have lists of genes, and instead of going 1 by 1 to get their location, can I add, ex 150 gene names, and blast them to get a list of their chromo location?

Anyway tips on how to do this faster than 1 by 1?

Thanks
Serge

Serge McGraw, PhD

 

Stagiaire postdoctoral

Laboratoire du Dr. Jacquetta Trasler

Institut de Recherche de l'Hôpital de Montréal pour Enfants
Département de Génétique Humaine, Université McGill

Place Toulon, # 222
4060, Rue Ste-Catherine Ouest
Montréal, Québec H3Z 2Z3

 

Postdoctoral fellow
Dr. Jacquetta Trasler's laboratory
Montreal Children's Hospital Research Institute
Department of Human Genetics, McGill University
Place Toulon, # 222
4060, Ste-Catherine West Street
Montreal, Quebec H3Z 2Z3

T:  514-412-4400, ext: 23291
F:  514-412-4331
E:  Serge....@mail.mcgill.ca

[Matthew Speir]

Hello Serge,

You can easily get the genomic coordinates for a list of genes using the table browser, http://genome.ucsc.edu/cgi-bin/hgTables. First, select the correct table and track that corresponds to the list of identifiers or names. Below those selections, you should see a line called "identifiers (names/accessions)" and here you can paste in your list of names or upload a file that contains all of the names. You have several different output options, including a bed file or hyperlinks to those positions in the genome browser. For more help on using the table browser, you can refer to the help page, http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. OpenHelix also has a free video tutorial that explains how to use the table browser and a few other tools at http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28.

For background about the different Gene Prediction tracks you may want to review the individual description pages. For example, there are the RefSeq genes http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=refGene, ENSEMBL genes http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=ensGene , and UCSC genes http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene Gene Prediction tracks that each use the corresponding refGene, ensGene and knownGene tables. In the Table Browser you can also click the "describe table schema" button to learn more about a selected table. The UCSC genes track includes the knownCanonical table, which with a few rare exceptions, contains one transcript per gene (usually the longest splice variant). UCSC genes also includes a cross reference table, "kgXref", which includes a "geneSymbol" field, which can be included when clicking "get output" in the Table Browser by choosing the “selected fields from primary and related tables” as your output type and checking the box next to kgXref.geneSymbol.

I hope this helps. If you have further questions or comments, please reply to gen...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--