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Created on: 09-Sep-2012   Last updated on: 09-Sep-2012  |  How to cite this?
Total resources - 30
A list of resources for transcription factors and binding sites
Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
DBD - Transcription factor prediction database
http://www.transcriptionfactor.org
1
Predicting transcription factor binding sites in DNA sequences
20
CREB Target Gene Database
http://natural.salk.edu/CREB
67
DATF - Database of Arabidopsis Transcription Factors
http://datf.cbi.pku.edu.cn
67
SIGNAL SCAN
http://www.dna.affrc.go.jp/sigscan/signal.html
Program that scans DNA sequences for eukaryotic transcriptional elements
84
TFCat
http://www.tfcat.ca
Curated catalog of mouse and human transcription factors
84
TRRD - Transcription Regulatory Regions Database
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
Information on structural and functional organization of transcription regulatory regions of eukaryotic genes
84
TFSEARCH - Searching Transcription Factor Binding Sites
http://www.cbrc.jp/research/db/TFSEARCH.html
88
rVISTA
http://rvista.dcode.org
Evolutionary analysis of transcription factor binding sites
95
AnimalTFDB
http://www.bioguo.org/AnimalTFDB
Genome-wide TFs in sequenced animal genomes
100
Cis-Finder - Cis Elements Finder
http://genomenetwork.nig.ac.jp/cisfinder
100
CONREAL
http://conreal.niob.knaw.nl
Identification of transcription factor binding sites (TFBS) that are conserved between two [orthologous promoter] sequences
100
cREMaG
http://www.cremag.org
Detection of the over-representation of transcription factor binding sites
100
DBTSS - DataBase of Transcriptional Start Sites
http://dbtss.hgc.jp
Represents exact positions of transcriptional start sites in the genome
100
GeneACT
http://promoter.colorado.edu/geneact
Characterize the regulatory regions of the genes of interest
100

URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016)
100
JASPAR
http://jaspar.genereg.net
Curated, non-redundant, transcription factor binding sites for eukaryotes
100
ooTFD - object-oriented Transcription Factors Database
http://www.ifti.org/ootfd
100
oPOSSUM
http://www.cisreg.ca/oPOSSUM
Detection of over-represented transcription factor binding sites in the promoters of sets of genes
100
PAINT - Promoter Analysis and Interaction Network Toolset
http://www.dbi.tju.edu/dbi/tools/paint
Find Transcription Factor (TF) binding sites on the sequences
100
PASTAA
http://trap.molgen.mpg.de/cgi-bin/pastaa.cgi
Identifying transcription factors associated with sets of co-regulated genes
100
STIFDB - Stress Responsive TranscrIption Factor Database
http://caps.ncbs.res.in/stifdb
Collection of abiotic stress responsive genes in Arabidopsis thaliana, and probable transcription factor binding sites in their promoters
100
TFCONES - Transcription Factor genes & associated COnserved Noncoding ElementS
http://tfcones.fugu-sg.org
100
Tfe - Transcription factor encyclopedia
http://www.cisreg.ca/cgi-bin/tfe/home.pl
100
TFSCAN
http://services.cbib.u-bordeaux2.fr/pise/tfscan.html
Scans DNA sequences for transcription factors
100
TRANSFAC®
http://www.gene-regulation.com/pub/databases.html
Transcription factors and their DNA binding sites
100
TRED - Transcriptional Regulatory Element Database
http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
100
TrSDB
http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
Proteome database of transcription factors
100
Weeder Web
http://159.149.109.9/modtools
Finding transcription factors regulating a set of genes
100

URL not working as on 27 Jan 2014 (confirmed on 15 Nov 2016)
YMF
http://frizzled.cs.washington.edu/YMF
Program for discovery of novel transcription factor binding sites
100
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