[Genome] identifying genes...

[Kayla Smith]

Johnathan,

It sounds like you have the correct strategy when you describe using the
Table Browser to intersect a gene track with your custom track.  However,
I notice that you say you're using "genes and gene prediction tracks".
That is actually subsection of the tracks we have available, and an
individual track/table is used in the intersection.  Once you've chosen
"genes and gene prediction tracks" you have to also choose which
track/table it is that you will be using.  I recommend using track "UCSC
genes" and table: "knownGene".   Also check that you have the "region"
option set to "genome" as this could be a reason your results are limited.

I hope this is helpful to you.  Please don't hesitate to write back if you
require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

On Thu, 5 Jul 2007, JONATHAN COOPER wrote:

> Hi There,
>
>   I am trying to identify genes associated with particular genomic intervals, but not having much luck. I have uploaded a file of RE1 transcription factor binding site coordinates into the table browser, and am trying to identify any genes that surround these sites (using "gene and gene prediction tracks") and intersecting it with my custom track. However, from the 60 odd sites in my track, only 4 genes have been identified. Is there something i am doing wrong? I was hoping to get a list of genes identified near each site that i could then cross-reference to find out functional information about.
>
>   If you have any suggestions i'd be very grateful.
>
>   best regards,
>   jonathan cooper
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