[Genome] how to identify transcription factors

[Archana Thakkapallayil]

Hello Irfan,

I am not sure that I understand your question correctly. From your 
question you could be asking two things:
a. You are trying to map a gene identifier to the transcription factor 
that it encodes.
b. By 'associated with' you mean the TF or TFs that might regulate a 
given gene.

If I assume you are trying to map a gene identifier to the transcription 
factor that it encodes, then I can explain you an easy way of getting 
this information from the Table Browser, using two tables, kgXref and 
tfbsConsFactors. All binding factors that are known to bind to the 
particular binding matrix of the binding site are listed along with 
their species, SwissProt ID, and a link to that factor's page on the 
UCSC Protein Browser if such an entry exists. This information can be 
obtained from the table 'tfbsConsFactors'. So if you have the name of a 
gene, you could get the corresponding SwissProt ID from the table kgXref 
and using this SwissProt ID you can extract the Transcription Factor 
associated with that gene.

1. To do this, first select the "kgXref" table under the 'tracks:Known 
Genes'. Click the filter "Create" button, then enter your gene id into 
the "kgID" text field. You could also use the "paste list" function if 
you have a list of gene IDs. Click Submit.  Then choose 'output format: 
selected fields from primary and related tables' and click 'get output'. 
Now on this page check the box 'spID' and click 'get output'. This gives 
you the SwissProt ID for your gene name.

2. Now back on the Table Browser select 'Group: Expression and 
Regulation'; 'track: TFBS Conserved'; 'table: tfbsConsfactors' and then 
enter the SwissProt ID into the "id" text field after clicking the 
"filter" button. Then hit "submit" button. Now choose 'output format: 
selected fields from primary and related tables' and click 'get output'. 
On this page check the box 'factor' and click 'get output'. This gives 
you the Transcription Factor associated with your gene.

If this is not what you are trying to accomplish, please feel free to 
write back.

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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>