Transcriptional regulator site and transcription factor (TF) databases for analyzing omic data.
Curators: Aziz Khan and Alvaro Sebastian
Animal Transcription Factor DataBase
Animal Transcription Factor DataBase
AnimalTFDB
A comprehensive database including classification and annotation of genome-wide…
A comprehensive database including classification and annotation of genome-wide transcription factors (TFs), transcription co-factors and chromatin remodeling factors in 65 animal genomes. The TFs are further classified into 70 families based on…
Arabidopsis Gene Regulatory Information Server
Arabidopsis Gene Regulatory Information Server
AGRIS
An information resource of Arabidopsis promoter sequences, transcription factors and…
An information resource of Arabidopsis promoter sequences, transcription factors and their target genes.
AtProbe
AtProbe
Focuses on specific binding elements on known genes, found with experimental methods.
Focuses on specific binding elements on known genes, found with experimental methods.
ChIPBase
ChIPBase
An integrated resource and platform for decoding transcription factor binding maps,…
An integrated resource and platform for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs (snoRNAs, tRNAs, snRNAs, etc.) and…
cisRED
cisRED
Holds conserved sequence motifs identified by genome scale motif discovery, similarity,…
Holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations.
CistromeFinder
CistromeFinder
Data portal that can help query, evaluate and visualize publicly available Chromatin…
Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse.
CistromeMap
CistromeMap
A knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and…
A knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human.
CollecTF
CollecTF
Compiles data on experimentally validated, naturally occurring transcription factors…
Compiles data on experimentally validated, naturally occurring transcription factors binding sites (TFBS) across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored…
CoryneRegNet
CoryneRegNet
The reference database and analysis platform for corynebacterial transcription factors…
The reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.
Cscan
Cscan
A web resource that includes a large collection of genome-wide ChIP-Seq experiments…
A web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others.
CTCFBSDB 2.0
CTCFBSDB 2.0
A database for CTCF binding sites and genome organization.
A database for CTCF binding sites and genome organization.
Database of Arabidopsis Transcription Factors
Database of Arabidopsis Transcription Factors
DATF
Collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and…
Collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.
Database of Poplar Transcription Factors
Database of Poplar Transcription Factors
DPTF
A plant transcription factor (TF) database containing 2576 putative poplar TFs…
A plant transcription factor (TF) database containing 2576 putative poplar TFs distributed in 64 families. These TFs were identified from both computational prediction and manual curation. We have provided extensive annotations including sequence…
Database of Rice Transcription Factors
Database of Rice Transcription Factors
DRTF
A collection of known and predicted transcription factors of Oryza sativa L. ssp. indica…
A collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica.
DAtabase of Transcription Factors with Alignments…
DAtabase of Transcription Factors with Alignments and Primers
DATFAP
A database of transcription factors from 13 plant species, and PCR primers for around 90%…
A database of transcription factors from 13 plant species, and PCR primers for around 90% of them.
DataBase of Transcriptional Start Sites
DataBase of Transcriptional Start Sites
DBTSS
It was originally constructed as a collection of uniquely determined transcriptional…
It was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, DBTSS has been regularly updated and in recent updates epigenetic information has also been…
DBD
DBD
A database of predicted transcription factors in completely sequenced genomes. The…
A database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the…
DBTBS
DBTBS
A reference database on transcriptional regulation in Bacillus subtilis, summarizing the…
A reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate.
ENCODE
ENCODE
The goal is to build a comprehensive parts list of functional elements in the human…
The goal is to build a comprehensive parts list of functional elements in the human genome.
EPDnew
EPDnew
A recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been…
A recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally characterized eukaryotic POL II promoters, which are…
Eukaryotic Promoter Database
Eukaryotic Promoter Database
EPD
An annotated non-redundant collection of eukaryotic POL II promoters, for which the…
An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.
FASTFORWARD DNA
FASTFORWARD DNA
A text-mining-assisted workflow to systematically extract knowledge about regulatory…
A text-mining-assisted workflow to systematically extract knowledge about regulatory interactions between human TFs from the biological literature. This workflow was applied to the entire Medline, which helped us to identify more than 45 000…
FlyFactorSurvey
FlyFactorSurvey
A database of DNA binding specificities for Drosophila transcription factors (TFs)…
A database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. FlyFactorSurvey provides community access to over 400 recognition motifs and position weight matrices for…
FlyTF
FlyTF
The Drosophila melanogaster transcription factor database.
The Drosophila melanogaster transcription factor database.
footprintDB
footprintDB
Predicts transcription factors which bind a specific DNA site or motif and DNA motifs or…
Predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein.
Grass Regulatory Information Server
Grass Regulatory Information Server
GRASSIUS
Provides a public web resource composed by a collection of databases, computational and…
Provides a public web resource composed by a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits.
Hematopoiesis Promoter Database
Hematopoiesis Promoter Database
HemoPDB
A comprehensive resource focused on transcriptional regulation during hematopoietic…
A comprehensive resource focused on transcriptional regulation during hematopoietic development and associated aberrances that result in malignancy.
hmChIP
hmChIP
A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse.
A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse.
Integrated Transcription Factor Platform
Integrated Transcription Factor Platform
ITFP
An integrated transcription factor (TF) platform that included abundant TFs and their…
An integrated transcription factor (TF) platform that included abundant TFs and their targets of mammalian. In short, ITFP will serve as an important resource for the research community of transcription and provide strong support for regulatory…
iTAK
iTAK
A program to identify plant transcription factors (TFs), transcriptional regulators (TRs)…
A program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. iTAK currently…
LegumeTFDB
LegumeTFDB
A public database that provides predicted transcription factor (TF) encoding genes…
A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula.
MachiBase
MachiBase
A one-stop service for Drosophila melanogaster transcription profiling.
A one-stop service for Drosophila melanogaster transcription profiling.
Mammalian Promoter Database
Mammalian Promoter Database
MPromDb
Integrates gene promoters with experimentally supported annotation of transcription start…
Integrates gene promoters with experimentally supported annotation of transcription start sites, cis-regulatory elements, CpG islands and chromatin immunoprecipitation microarray (ChIP-chip) experimental results with intuitively designed…
Mining Yeast Binding Sites
Mining Yeast Binding Sites
MYBS
A comprehensive web server that integrates an array of both experimentally verified and…
A comprehensive web server that integrates an array of both experimentally verified and predicted position weight matrixes (PWMs) from eleven databases.
Multi-genome Analysis of Positions and Patterns…
Multi-genome Analysis of Positions and Patterns of Elements of Regulation
MAPPER database
Contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream…
Contains putative Transcription Factor Binding Sites (TFBSs) located in the upstream sequences of genes from the human, mouse and D.melanogaster genomes.
NPEST
NPEST
A tool for the analysis of expressed sequence tags (EST) distributions and transcription…
A tool for the analysis of expressed sequence tags (EST) distributions and transcription start site (TSS) prediction. This method estimates an unknown probability distribution of ESTs using a maximum likelihood (ML) approach, which is then used to…
OnTheFly
OnTheFly
A systematic determination of Drosophila melanogaster transcription factor DNA-binding…
A systematic determination of Drosophila melanogaster transcription factor DNA-binding specificities.
P2CS
P2CS
A comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs).…
A comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation…
PAZAR
PAZAR
One stop shopping experience for transcription factors and regulatory sequence…
One stop shopping experience for transcription factors and regulatory sequence annotations. It is a software framework for the construction and maintenance of regulatory sequence data annotations.
PLACE
PLACE
A database of nucleotide sequence motifs found in plant cis-acting regulatory DNA…
A database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other…
Plant Promoter database
Plant Promoter database
PlantProm
Initially developed as an annotated, non-redundant collection of proximal promoter…
Initially developed as an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.
Plant Transcription Factor Database
Plant Transcription Factor Database
PlantTFDB
A portal for the functional and evolutionary study of plant transcription factors.
A portal for the functional and evolutionary study of plant transcription factors.
Plant Transcription Factor Database
Plant Transcription Factor Database
PlnTFDB
A public database arising from efforts to identify and catalogue all Plant genes involved…
A public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.
PlanTAPDB
PlanTAPDB
A phylogeny-based comprehensive resource of plant transcription associated proteins.
A phylogeny-based comprehensive resource of plant transcription associated proteins.
PlantTFcat
PlantTFcat
A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR…
A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences.
ppdb
ppdb
A plant promoter database that provides information on transcription start sites (TSSs),…
A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements.
Predicted Prokaryotic Regulatory Proteins
Predicted Prokaryotic Regulatory Proteins
P2RP
Enables users to identify and annotate transcription factors (TFs) and two-component…
Enables users to identify and annotate transcription factors (TFs) and two-component system (TCS) proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the…
Predicted Prokaryotic Transcription Factors
Predicted Prokaryotic Transcription Factors
P2TF
An integrated and comprehensive database relating to transcription factor proteins. The…
An integrated and comprehensive database relating to transcription factor proteins. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access…
PReMod
PReMod
Describes more than 100,000 computational predicted transcriptional regulatory modules…
Describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome.
PRODORIC
PRODORIC
A comprehensive database about gene regulation and gene expression in prokaryotes.
A comprehensive database about gene regulation and gene expression in prokaryotes.
ProTISA
ProTISA
Intended to collect confirmed translation initiation sites (TISs) for prokaryotic genomes.
Intended to collect confirmed translation initiation sites (TISs) for prokaryotic genomes.
REDfly
REDfly
A curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs)…
A curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).
RegPrecise
RegPrecise
A database for capturing, visualization and analysis of transcription factor regulons…
A database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by the comparative genomic approach in a wide variety of prokaryotic genomes.
REGULATOR
REGULATOR
A metazoan transcription factor and maternal factor resource specially designed for…
A metazoan transcription factor and maternal factor resource specially designed for developmental biology studies. Using this web interface, users can browse, search, and download detailed information on species of interest, genes, transcription…
RegulonDB
RegulonDB
A relational database that offers, in an organized and computable form, updated knowledge…
A relational database that offers, in an organized and computable form, updated knowledge on transcriptional regulation in Escherichia coli K-12. Its electronic format enables researchers to compare their results with the legacy of previous…
RIKEN Arabidopsis Transcription Factor database
RIKEN Arabidopsis Transcription Factor database
RARTF
Database and Tools for Complete Sets of Arabidopsis Transcription Factors.
Database and Tools for Complete Sets of Arabidopsis Transcription Factors.
ScerTF
ScerTF
Catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription…
Catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors.
SCPD
SCPD
A comprehensive yeast-specific promoter database.
A comprehensive yeast-specific promoter database.
Small Molecule-Transcription Factor
Small Molecule-Transcription Factor
SM-TF
A structural database of small molecule-transcription factor complexes. The 3D structures…
A structural database of small molecule-transcription factor complexes. The 3D structures of the co-bound small molecule and the corresponding binding sites on transcription factors (TFs) are provided in the database, serving as a valuable resource…
SoyDB
SoyDB
A Knowledge Database of Soybean Transcription Factors.
A Knowledge Database of Soybean Transcription Factors.
Stress Responsive Transcription Factor Database
Stress Responsive Transcription Factor Database
STIFDB
A comprehensive collection of biotic and abiotic stress responsive genes in Arabidopsis…
A comprehensive collection of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters.
SwissRegulon
SwissRegulon
The database contains genome-wide annotations of regulatory sites.
The database contains genome-wide annotations of regulatory sites.
Targetfinder.org
Targetfinder.org
Provides a web-based resource for finding genes that show a similar expression pattern to…
Provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13,000 genes). The primary application of…
TcoF
TcoF
A database that facilitates the exploration of proteins involved in the regulation of…
A database that facilitates the exploration of proteins involved in the regulation of transcription in humans.
TFCat
TFCat
A curated catalog of mouse and human transcription factors (TF) based on a reliable core…
A curated catalog of mouse and human transcription factors (TF) based on a reliable core collection of annotations obtained by expert review of the scientific literature. Annotated genes are assigned to a functional category and confidence level.…
TFClass
TFClass
Aims at classifying eukaryotic transcription factors (TFs) according to their DNA-binding…
Aims at classifying eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs). For this, a classification schema comprising four generic levels (superclass, class, family and subfamily) was defined that could accommodate…
TFinDIT
TFinDIT
Transcription Factor-DNA Interaction Data Depository.
Transcription Factor-DNA Interaction Data Depository.
TOBFAC
TOBFAC
It came into being as a database of tobacco transcription factors at the time, possibly…
It came into being as a database of tobacco transcription factors at the time, possibly the largest collection of transcription factor sequences from a single plant species (over 2,500 genes).
Tractor_DB
Tractor_DB
Contains a collection of computationally predicted Transcription Factors' binding…
Contains a collection of computationally predicted Transcription Factors' binding sites in gamma-proteobacterial genomes.
TRANSFAC
TRANSFAC
Provides data on eukaryotic transcription factors, their experimentally-proven binding…
Provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. TRANSCompel contains data on eukaryotic transcription factors experimentally…
TreeTFDB
TreeTFDB
Provides the complete transcription factor (TF) repertoires of 6 genome sequenced tree…
Provides the complete transcription factor (TF) repertoires of 6 genome sequenced tree species: papaya, jatoropha, cassava, poplar, castor bean and grape vine from annotated genes on each genome.
TrSDB
TrSDB
A proteome database of eukaryotic transcription factors based upon predicted motifs by…
A proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Extensive and diverse information for each database entry, different analyses…
WebGeSTer DB
WebGeSTer DB
It comprises of >2,200,000 bacterial terminators identified from a total of 2036…
It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids.
Yeast Promoter Atlas
Yeast Promoter Atlas
YPA
A repository of promoter features in Saccharomyces cerevisiae.
A repository of promoter features in Saccharomyces cerevisiae.
Yeast Search for Transcriptional Regulators And…
Yeast Search for Transcriptional Regulators And Consensus Tracking
YEASTRACT
A curated repository of more than 206000 regulatory associations between transcription…
A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references.
Yeast Transcription Factor Specificity Compendium
Yeast Transcription Factor Specificity Compendium
YeTFaSCo
A collection of all available TF specificities for the yeast Saccharomyces cerevisiae in…
A collection of all available TF specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.
Yeast Transcriptional Regulatory Pathway
Yeast Transcriptional Regulatory Pathway
YTRP
Database for yeast biologists with these comprehensive transcriptional regulatory pathway…
Database for yeast biologists with these comprehensive transcriptional regulatory pathway (TRP) information and the accompanying literature supports for the TRPs.