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Question: Transcription Factor And Corresponding Target Gene Resources
4
gravatar for Woa
5.0 years ago by
Woa • 2.7k
United States
Woa • 2.7k wrote:

Hello I'm looking for transcription factor resource that would give a list of transcription factors and their corresponding target gene(s).

The species I'm mostly interested in are Mouse and Rat.

I've found this database but there can be a better resource.

http://itfp.biosino.org/itfp/TFViewer/mouse_tf.jsp?table=mouse_tf&page=1

Thanks
gene transcription target • 4.1k views
ADD COMMENT • link •
modified 5.0 years ago by Charles Warden ♦ 5.0k • written 5.0 years ago by Woa • 2.7k
4
gravatar for Charles Warden
5.0 years ago by
Charles Warden ♦ 5.0k
Duarte, CA
Charles Warden ♦ 5.0k wrote:

In general, there are databases like TRANSFAC and JASPAR for transcription factor binding motifs, and various tools that utilize the matrices present in those databases.

I think this interface provides the functionaity that you are looking for:

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

More commonly, I tend to work with lists of differentially expressed genes, and I am looking for what motifs are enriched in a given gene list. GATHER is one good, open-source tool for doing this (although there certainly are others):

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

If you are interested in de novo prediction of enriched motifs, I would recommend SCOPE:

http://genie.dartmouth.edu/scope/
ADD COMMENT • link written 5.0 years ago by Charles Warden ♦ 5.0k
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