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database name description class url
MAPPER2 The MAPPER Database?contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. the human, mouse and D.melanogaster genomes http://genome.ufl.edu/mapperdb
JASPAR The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc) consist of the open data acess, non-redundancy and quality. Eukaryotes http://jaspar.genereg.net/
DBTBS DBTBS is a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights Bacillus subtilis http://dbtbs.hgc.jp/
RegulonDB All the transcriptional regulatory information of E.coli. E. coli http://regulondb.ccg.unam.mx/
RegTransBase RegTransBase consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. bacteria http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main
PRODORIC PRODORIC? is a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. A variety of bioinformatics tools for the prediction, analysis and visualization of regulons and gene reglulatory networks is included. prokaryotes http://prodoric.tu-bs.de/
RegPrecise 3.0 RegPrecise 3.0 is resource for genome-scale exploration of transcriptional regulation in bacteria Bacteria http://regprecise.lbl.gov/RegPrecise/
TRANSFAC TRANSFAC provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. eukaryotic http://www.gene-regulation.com/pub/databases.html
PLACE PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. Plants http://www.dna.affrc.go.jp/PLACE/index.html
ATCOECIS cis-regulatory elements in Arabidopsis. Arabidopsis http://bioinformatics.psb.ugent.be/ATCOECIS/download.htpl
Paper In the field of molecular biology, the ETS (E-twenty six) family is one of the largest families of transcription factors and is unique to metazoans human and mouse http://www.nature.com/emboj/journal/v29/n13/full/emboj2010106a.html
Paper Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites Human http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852749/
Paper FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system Human http://nar.oxfordjournals.org/content/early/2010/11/19/nar.gkq858.full
Paper Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity Mammalian http://www.cell.com/retrieve/pii/S0092867405013954?cc=y
Paper Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Mammalian http://www.ncbi.nlm.nih.gov/pubmed/22189060
Paper Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities Human,Mouse http://genome.cshlp.org/content/20/6/861
Paper Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells Mouse http://www.sciencedirect.com/science/article/pii/S009286740800617X
UNIPROBE Mouse TF motifs Mouse http://the_brain.bwh.harvard.edu/uniprobe/downloads.php
Paper Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences Eukaryotic http://www.cell.com/retrieve/pii/S0092867408006831
MacIsaac v1 Yeast motifs from the?Sacharomyces Cerevisiae Promoter Database Yeast http://fraenkel.mit.edu/improved_map/
Pollard v2 Drosophila Sequence Specific Transcription Factor Binding Site Matrices Drosophila http://www.danielpollard.com/matrices.html
Paper Motif discovery and motif finding from genome-mapped DNase footprint data. Drosophila http://fraenkel.mit.edu/improved_map/
CollecTF CollecTF is a database of transcription factor binding sites (TFBS) in the Bacteria domain. Bacteria http://collectf.umbc.edu/home/greet/