Question: Mapping Transcription Factors To Genes
1
gravatar for Min
5.0 years ago by
Min20
Min20 wrote:

Dear all,

I'm trying to map transcription factor matrix id to gene symbol.

(eg.

TRANSFAC matrix id -> gene symbol (official)

V$SRF_Q4 -> SRF

V$TGIF_01 -> IL10

V$AP1_01 -> ???, ???, ???, ...

V$MTATA_B -> ???

)

I have trouble with some matrices that use not approved symbols as identifier. (like above question marks)

I found AP1 composed of multiple genes, which are FOS, FOSB, JUN, JUNB, JUND here http://rulai.cshl.edu/TRED/TFlist.htm

but I can't find any other database including whole transcription factors that are made up multiple genes.

And I wonder where can I found list of this unofficial symbols that describe transcription factors.

Also, I wonder why this unmatched happen occurs.

WARNING: I'm NOT find transcription factor binding site. I just want to gene symbols of transcription factors themselves.

thanks a lot!

gene multiple transcription • 2.7k views
ADD COMMENTlink modified 3.9 years ago by huangziyan111110 • written 5.0 years ago by Min20

Dear min,

   I am still confused about how to do with  mapping transcription factor matrix id to gene symbol.Could you tell

me ?

Thank you

ADD REPLYlink written 3.9 years ago by huangziyan111110
1
gravatar for Charles Warden
5.0 years ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

I think you need to directly go to the TRANSFAC database:

http://www.biobase-international.com/gene-regulation (free version)

http://www.biobase-international.com/product/transcription-factor-binding-sites (commerical version info)

If I use the TRANFAC enrichment tool in GATHER, this is where the hyperlink leads (and some TFs already have descriptions):

http://gather.genome.duke.edu/

Also, this link provides a list of alternative names for TFs in TRED (for human, mouse , or rat), but it isn't easy to search (it is organized by official gene symbol, and it isn't ordered alphabetically):

http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=dataBrowseForm

ADD COMMENTlink written 5.0 years ago by Charles Warden6.5k

Thanks a lot.

I think I didn't carefully consider this. now I got what I have to do. Thanks for your help.

ADD REPLYlink written 5.0 years ago by Min20
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