Transcription Factor And Corresponding Target Gene Resources
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11.4 years ago
Woa ★ 2.9k

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 • 6.0k views
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4
Entering edit mode
11.4 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/

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