Transcription Regulation

List of Transcriptional regulator sites and transcription factors Databases at Nucleic Acid Research.

http://www.oxfordjournals.org/nar/database/subcat/1/4

TRANSFAC contains data on transcription factors, their experimentelly-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices.

http://www.gene-regulation.com/pub/databases.html

PathoDB

PathoDB� 2.0 Public 2005 is a database on pathologically relevant mutated forms of transcription factors and their binding sites.

http://www.gene-regulation.com/pub/databases.html

EPD

The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.

http://www.epd.isb-sib.ch/

DBTBS

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

http://dbtbs.hgc.jp/

PlnTFDB

ChlamyTFDB (1.0) is a public database arising from efforts to identify and catalogue all Chlamydomonas reinhardtii genes involved in transcriptional control.

http://plntfdb.bio.uni-potsdam.de/v3.0/

TRED

PlnTFDB (3.0) is a public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.

http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home

TrSDB

A Proteome Database of Transcription Factors

http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl

OTFBS

Over-represented Transcription Factor Binding Site Prediction Tool is a method base on TRANSFAC Matrix, it can detect over-represented motifs of known transcription factors from a set of related sequences. Particularly, promoters of a same gene family or from the same tissue can be submitted as a analysis subject. Promoters of putative co-regulated genes clustered with gene expression data should be also a good candidate to analysis.

http://www.bioinfo.tsinghua.edu.cn/~zhengjsh/OTFBS/

JASPAR

The high-quality transcription factor binding profile database

http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl

Dna Block Aligner

Compares two DNA sequences assuming colinear blocks, ideal for promoters.

http://www.ebi.ac.uk/Tools/Wise2/dbaform.html

PromoterWise

Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

http://www.ebi.ac.uk/Tools/Wise2/promoterwise.html

Promoter Prediction

An online tool using Neural Network Promoter Prediction version 2.2

http://www.fruitfly.org/seq_tools/promoter.html

WWW Promoter Scan

Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.

http://www-bimas.cit.nih.gov/molbio/proscan/

Promoter 2.0

Promoter2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions. It builds on principles that are common to neural networks and genetic algorithms.

http://www.cbs.dtu.dk/services/Promoter/

PromoSer

Human, Mouse and Rat promoter extraction service

http://biowulf.bu.edu/zlab/PromoSer/

SAK

Prokaryotic promoter analysis

http://nostradamus.cs.rhul.ac.uk/%7Eleo/sak_demo/

nmeta

Analysis of the promoter sequence of genes using TF-maps (maps of predicted transcription factors)

http://genome.imim.es/software/mmeta/index.html