[Genome] how to identify transcription factors

[Archana Thakkapallayil]

Hi Irfan,

I have forwarded your question to the person who developed this track. I 
will get back to you when I have more information.

In the mean time if you have any other questions please don't hesitate 
to contact us again.

Regards,

Archana
UCSC Genome Bioinformatics Group


Irfan Qureshi wrote:
> Hi everyone-
> I'm wondering if I'm doing this right or if there is a better way to  
> identify the TF associated with a given gene.
> Thanks
>
>
> Using the Table Browser
>
> 1.  select the following
> Group: known gene
> Track: known gene
> Identifier- enter the gene of interest (ie NM_X)
> Output- custom track
> whole gene or upstream ? (I'm unsure what to select here)
>
> 2.  select the following
> Group: expression and regulation
> Track: tfbs
> Table cons_sites
> Intersect with custom track from 1
> Output: custom track
> whole gene? (I'm also unsure what to select here)
>
> 3.  select the following
> Group: custom track
> Track: select custom track from 2
> clear intersection
> Output get selected fields- name of tfbs (ie V$X)
>
> 4.  select the following
> Group expression and regulation
> Track: tfbs
> Table: cons_factors
> Filter: enter names of tfbs from 3
> Output: selected fields from table
> choose "actors (ie myc)
>
>
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