Transcription Factor And Corresponding Target Gene Resources
1
4
Entering edit mode
8.0 years ago
Woa ★ 2.8k

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

transcription target gene • 5.2k views
ADD COMMENT
4
Entering edit mode
8.0 years ago

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

Login before adding your answer.

Traffic: 1857 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6