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Transcription factors
Note that some species-specific databases were moved to the Species-specific transcription factor databases article.
User may also find the article on Gene Expression and Regulation useful.
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GenomeTrafac is a whole genome resource for the detection of transcription factor binding site clusters associated with conventional RNA-encoding genes and microRNA encoding genes conserved between mouse and human gene orthologs. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. GenomeTrafac can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and allows consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. The system identifies validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes. <pubmed argument="GenomeTrafac">17178752</pubmed>
Tractor_DB
Stores computationally predicted transcription factors' binding sites in 30 gamma-proteobacterial genomes including Escherichia coli K12, Haemophilus influenzae, Salmonella typhi, S.typhimurium, Shewanella oneidensis, Shigella flexneri, Vibrio cholerae and Y.pestis. Useful to help in the design of microarray experiments and the interpretation of results, and studies of the Comparative Genomics of the regulatory networks of this group of organisms.
Users can retrieve information on the conservation of regulatory interactions in the 30 genomes included in the database by navigating a map that represents a core of the known Escherichia coli regulatory network. Tractor DB is mirrored in Brazil and Mexico <pubmed argument="Tractor_DB">17088283</pubmed>
MATCH
Match is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match is closely interconnected and distributed together with the TRANSFAC database. In particular, Match uses the matrix library collected in TRANSFAC and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team.<pubmed argument="MATCH">12824369</pubmed>
Promo
Identification of putative transcription factor binding sites in a species or groups of species of interest.
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TraFac
Regulatory Region Prediction. TraFaC (Transcription Factor binding site Comparison) is a web-accessible system developed by the Pediatric Informatics division of Cincinnati Childrens Hospital Medical Center for identifying regulatory regions using a comparative sequence analysis approach. It integrates analysis results from applications such as PipMaker (Schwartz et al., 2000) and MatInspector professional (Quandt et al., 1995) or Match and generates a graphical output. It locates matches in sequences of unlimited length. The program compares the MatInspector/Match output (showing a list of potential transcription factor (TF) binding sites) generated using DNA sequences and identifies conserved blocks of TF binding sites in the two sequences that are compared. This is done in the context of sequence similarity for which the PipMaker software is used. PipMaker generates a Percent Identity Plot (PIP) and a concise alignment file.
SiteSeer
Visualisation and analysis of transcription factor binding sites in nucleotide sequences. Tool for the visualisation of mapped transcription factor binding sites in the upstream regions of single or grouped eukaryotic genes, allowing users to examine the positions of known and user-defined sites. SiteSeer allows the user to map different sections of the TRANSFAC and SCPD databases (or a set of user-defined sites) onto nucleotide sequences. Additionally, users may restrict the analysis by expectation values for certain DNA words as well as by known binding sites specific to a given organism. We believe this tool will prove particularly valuable for biologists who wish to examine sets of co-expressed or functionally-related genes and those who wish to visualise the positions of promoter sequences and generate displays for publications.<pubmed argument="SiteSeer">12824368</pubmed>
BindGene
Search for transcription factor binding sites - especially those of the transcription factor HNF1A.
Target Explorer
Automated tool for the identification of new target genes for a specified set of transcription factors. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes.<pubmed argument="Target Explorer">12824372</pubmed>
BioProspector
Discovers conserved transcription factor binding sites among upstream sequences from co-regulated genes. BioProspector discovers conserved transcription factor binding sites among upstream sequences from co-regulated genes. BioProspector uses a Gibbs sampling approach to align and score DNA segments. It can find short (8bp), interrupted, weakly conserved (50%) and not very abundant DNA motifs from microarray data.
TRANSPATH
TRANSPATH is a database system about gene regulatory networks that combines detailed information on signal transduction with tools for visualisation and analysis. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signalling pathways from ligand to target genes and their products, which may themselves be involved in regulatory action.
JASPAR
An open-access database for eukaryotic transcription factor binding profiles. The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions.<pubmed argument="JASPAR">14681366</pubmed>
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Dragon ERE Finder 2
Tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. <pubmed argument="Dragon ERE Finder 2">12824376</pubmed>
YMF
Program for discovery of novel transcription factor binding sites by statistical overrepresentation. YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores.<pubmed argument="YMF">12824371</pubmed>
OTFBS
Over-represented Transcription Factor Binding Site Prediction Tool. Genes of the same family or from the same tissue are often similarily regulated . An assumption can be made that their promoters might share a set of binding sites of a same set of Transcription Factors. OTFBS 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 might also be a good candidate to analysis.
TrSDB
TranScout Database - proteome database of transcription factors. Proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Nine eukaryotic proteomes are included in the current version. Extensive and diverse information for each database entry, different analyses considering TranScout classification and similarity relationships are offered for research on transcription factors or gene expression.<pubmed argument="TrSDB">14681387</pubmed>
AraC-XylS
A database of a family of helix-turn-helix transcription factors of bacteria.
Transcription factor - Wikipedia
Categories. : Wikipedia articles needing clarification. Gene expression. Views. Article. Discussion. Edit this page. History.. Personal tools. Sign in / create account.. Navigation. Main Page. Community Portal. Featured articles. Current ...
Basal Transcription Factors
Basal Transcription Factors Basal Transcription Factor Information. I'm slowly trying to build a WWW database for information about the eukaryotic transcription machinery. It's intended primarily for people in the field, but may be useful ...
TRED - Transcriptional Regulatory Element Database
Features relatively complete genome wide promoter annotation for human, mouse and rat, availability of transcription factor binding and regulation information, relative data accuracy, flexible data retrieval & sequence analysis tools. TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, those regulatory elements are mapped on to the assembled genomes. Latest release (2006) includes 36 TF families involved in cancer, Includes 11,660 target genes target promoters and genes for TF families, and 14,908 target promoters in human, mouse and rat. Includes GRNs for each TF family by connecting the TF–target gene pairs to help detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research. <pubmed argument="TRED">17202159</pubmed>
The Gibbs Motif Sampler Homepage
The Gibbs Motif Sampler Homepage. Welcome to the Gibbs Motif Sampler Homepage. The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences. This software was developed by Eric C. Rouchka and ...
TREG-Comparator
This web application allows you to compare a set of position weight matrices (PWM) against the T-Reg database! T-Reg is a relational database on transcriptional regulation that contains a collection of PWMs.
TRANSCompel
Composite regulatory elements. TRANSCompel is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signalling pathways.
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