1.TRANSFAC: The Transcription Factor Database
http://gene-regulation.com/pub/databases.html#transfac

2.JASPAR: The high-quality transcription factor binding profile database
http://jaspar.genereg.net/

3.UniPROBE: transcription factor binding site matrices based on the universal protein binding microarray (PBM) technology
http://the_brain.bwh.harvard.edu/uniprobe/

4.HT-SELEX
http://ccg.vital-it.ch/htpselex/

5.CisBP: the online library of transcription factors and their DNA binding motifs
http://cisbp.ccbr.utoronto.ca/

6. TFCat: The curated catalog of mouse and human transcription factors
http://www.tfcat.ca/

7.HumanTFs:  The Human Transcription Factors
http://humantfs.ccbr.utoronto.ca/

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Related databases
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1.EPD: The Eukarytic Promoter database
http://epd.vital-it.ch/index.php

2.myHITS:A database and web tools devoted to protein domains
https://myhits.isb-sib.ch/

3.CleanEx: A database which provides access to public gene expression data via unique approved gene symbols
http://cleanex.vital-it.ch/index.html

4.Motif Databases---MEME Suite
http://meme-suite.org/db/motifs
 
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