Table browser

[Jennifer Hauenstein]

Good morning~

I would like to use the table browser to create a list of genes, their OMIM numbers, and their short descriptions from a segment that I viewed in the genome browser. From the selections I chose, I keep getting multiple entries for each gene. Here are the selections I am normally choosing that give me the multiple gene output. Also, I would like to get the OMIM numbers but that track is greyed out. Which selections can I choose to get a single output of the gene name, description, and OMIM number for each gene in the segment?

Thanks~

Jen

[Robert Kuhn]

Hello, Jennifer,

Thanks for your question.  The OMIM tables are not accessible via the Table 

Browser if you have "genome" selected as a region, per our agreement with 

the OMIM team not to redistribute their entire dataset.  The DDX11L1 gene

in your output is the first gene on chr1 and your output is likely very large

(whole genome)?  Choose the button next to "position" to restrict your query 

to the chr3 region you were viewing on the Browser.  The OMIM tables should 

then be available to you.

The multiple entries are due to the fact that the knownGene table will give a result 

for each isoform.  If you wish one isoform per locus, use the knownCannonical

table in the UCSC Genes track.  Though I see in your image that you already

have that table selected, your output shows that the query you executed for that

particular output had the knownGene table selected.

The following video shows most of the process you request:

   https://www.youtube.com/watch?feature=player_detailpage&v=RjB_N1GpT0U&list=UUQnUJepyNOw0p8s2otX4RYQ

You may also be interested in the Data Integrator, which can do what the

Table Browser does but also a bit more.  Here is a short video demonstrating

almost the exact problem you describe, including obtaining OMIM data:

  https://www.youtube.com/watch?feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ

Best wishes, and thanks for using the Genome Browser.

   --b0b kuhn

  ucsc genome bioinformatics group

Browser training workshops available via:  http://genome.ucsc.edu/training

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