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Transcription factor databases | Protein sequence analysis

Transcriptional regulator site and transcription factor (TF) databases for analyzing omic data.

PlantTFDB
Dataset

PlantTFDB Plant Transcription Factor Database

A database of functional and evolutionary study of plant transcription factors.…

A database of functional and evolutionary study of plant transcription factors. With the version 4.0, PlantTFDB offers 320 370 TFs from 165 species. Three types of annotation provide more directly…

PLACE
Dataset

PLACE

A database of nucleotide sequence motifs found in plant cis-acting regulatory…

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…

RegulonDB
Dataset

RegulonDB

A relational database that offers, in an organized and computable form, updated…

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…

footprintDB
Dataset

footprintDB

Integrates several open access repositories of curated cis-elements, DNA…

Integrates several open access repositories of curated cis-elements, DNA motifs, and TFs into a unique repository. footprintDB systematically annotates the binding interfaces of the TFs by exploiting…

PlantRegMap
Dataset

PlantRegMap

A toolkit for the study of transcriptional regulation in plants. PlantRegMap…

A toolkit for the study of transcriptional regulation in plants. PlantRegMap provides a comprehensive, high-quality resource of plant transcription factors, regulatory elements and interactions…

TRANSFAC
Dataset

TRANSFAC

Provides data on eukaryotic transcription factors, their experimentally-proven…

Provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. TRANSCompel contains data…

DBTSS
Dataset

DBTSS DataBase of Transcriptional Start Sites

It was originally constructed as a collection of uniquely determined…

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…

AnimalTFDB
Dataset

AnimalTFDB Animal Transcription Factor DataBase

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…

PathoDB
Dataset

PathoDB

Provides information about pathologically relevant mutations in transcription…

Provides information about pathologically relevant mutations in transcription factor (TF) genes or in their binding sites (TFBS). PathoDB is a module of TRANSFAC, a database of TF and their…

TFClass
Dataset

TFClass

Aims at classifying eukaryotic transcription factors (TFs) according to their…

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…

DBD
Dataset

DBD

A database of predicted transcription factors in completely sequenced genomes.…

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…

TcoF-DB
Dataset
MAPPER database
Dataset
PathoYeastract
Dataset
PRODORIC
Dataset

PRODORIC PROcariotIC Database Of Gene-Regulation

Provides information about gene regulation and expression in prokaryotes.…

Provides information about gene regulation and expression in prokaryotes. PRODORIC is a manual curated data resource and bioinformatics tool platform database allowing browsing, prediction and…

RegTransBase
Dataset

RegTransBase

Consists of two modules - a database of regulatory interactions based on…

Consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. This literature based information in…

PlnTFDB
Dataset

PlnTFDB Plant Transcription Factor Database

A public database arising from efforts to identify and catalogue all Plant…

A public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.

DBTBS
Dataset

DBTBS

A reference database on transcriptional regulation in Bacillus subtilis,…

A reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate.

ChIPBase
Dataset

ChIPBase

Enables to explore the transcriptional regulatory networks of noncoding RNAs…

Enables to explore the transcriptional regulatory networks of noncoding RNAs (ncRNAs) and protein-coding genes (PCGs). ChIPBase is an open database that integrates many ChIPseq peak datasets of…

AGRIS
Dataset

AGRIS Arabidopsis Gene Regulatory Information Server

An information resource of Arabidopsis promoter sequences, transcription…

An information resource of Arabidopsis promoter sequences, transcription factors and their target genes.

REDfly
Dataset

REDfly

A curated collection of known Drosophila transcriptional cis-regulatory modules…

A curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).

FlyFactorSurvey
Dataset

FlyFactorSurvey

A database of DNA binding specificities for Drosophila transcription factors…

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…

PsychENCODE
Dataset

PsychENCODE

Represents an integrated collaborative effort in neuroscience and psychiatry to…

Represents an integrated collaborative effort in neuroscience and psychiatry to collectively analyze genomic regulatory elements in a large cohort of well-curated human brains. Key goals of the…

cisRED
Dataset

cisRED

Holds conserved sequence motifs identified by genome scale motif discovery,…

Holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations.

PReMod
Dataset

PReMod

Describes more than 100,000 computational predicted transcriptional regulatory…

Describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome.

PlantProm
Dataset

PlantProm Plant Promoter database

Initially developed as an annotated, non-redundant collection of proximal…

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…

CistromeMap
Dataset

CistromeMap

A comprehensive and consistently annotated knowledgebase of all published or…

A comprehensive and consistently annotated knowledgebase of all published or public ChIP-seq and DNase-seq data in mouse and human. In total, there are 2711 ChIP-Seq datasets for transcription and…

EPD
Dataset

EPD Eukaryotic Promoter Database

An annotated non-redundant collection of eukaryotic POL II promoters, for which…

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.

TFBSbank
Dataset

TFBSbank

A state-of-the-art and user-friendly platform which houses the annotation of…

A state-of-the-art and user-friendly platform which houses the annotation of 1870 chromatin immunoprecipitation (ChIP) data sets of 585 transcription factors (TFs) in 5 species (human, mouse, fly,…

SCPD
Dataset

SCPD

An yeast-specific promoter database. SCPD provides access to yeast genes,…

An yeast-specific promoter database. SCPD provides access to yeast genes, regulatory elements and transcriptional factors, but also to analysis tools. It retrieves promoter sequences, search for…

DATF
Dataset

DATF Database of Arabidopsis Transcription Factors

Collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene…

Collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.

FlyMine
Dataset

FlyMine

The Drosophila melanogaster transcription factor database.

The Drosophila melanogaster transcription factor database.

YeTFaSCo
Dataset

YeTFaSCo Yeast Transcription Factor Specificity Compendium

A collection of all available TF specificities for the yeast Saccharomyces…

A collection of all available TF specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.

ppdb
Dataset

ppdb

A plant promoter database that provides information on transcription start…

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…

ScerTF
Dataset

ScerTF

Catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast…

Catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors.

WebGeSTer DB
Dataset

WebGeSTer DB

It comprises of >2,200,000 bacterial terminators identified from a total of…

It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids.

CTCFBSDB
Dataset

CTCFBSDB

A database for CTCF binding sites and genome organization.

A database for CTCF binding sites and genome organization.

TcoF
Dataset

TcoF

A database that facilitates the exploration of proteins involved in the…

A database that facilitates the exploration of proteins involved in the regulation of transcription in humans.

MYBS
Dataset

MYBS Mining Yeast Binding Sites

A comprehensive web server that integrates an array of both experimentally…

A comprehensive web server that integrates an array of both experimentally verified and predicted position weight matrixes (PWMs) from eleven databases.

YPA
Dataset

YPA Yeast Promoter Atlas

Collects promoter features in Saccharomyces cerevisiae. YPA integrates…

Collects promoter features in Saccharomyces cerevisiae. YPA integrates resources such as transcription start sites (TSSs), TATA boxes, transcription factor binding sites (TFBS), nucleosome occupancy,…

MachiBase
Dataset

MachiBase

Gives access to Drosophila melanogaster 5’-end mRNA tags at different…

Gives access to Drosophila melanogaster 5’-end mRNA tags at different developmental states. MachiBase is designed to assist fly biologists in their analyses of gene expression and in placing…

GRASSIUS
Dataset

GRASSIUS Grass Regulatory Information Server

Provides a public web resource composed by a collection of databases,…

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…

CoryneRegNet
Dataset

CoryneRegNet

The reference database and analysis platform for corynebacterial transcription…

The reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. CoryneRegNet also provides easy-to-use functions that allow the user to submit…

DRTF
Dataset

DRTF Database of Rice Transcription Factors

A collection of known and predicted transcription factors of Oryza sativa L.…

A collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica.

RARTF
Dataset
PlanTAPDB
Dataset

PlanTAPDB

A phylogeny-based comprehensive resource of plant transcription associated…

A phylogeny-based comprehensive resource of plant transcription associated proteins.

CR Cistrome
Dataset

CR Cistrome Chromatin Regulator Cistrome

A ChIP-seq database containing information on chromatin regulators (CRs) and…

A ChIP-seq database containing information on chromatin regulators (CRs) and CR-histone modification (HM) linkages in human and mouse, and it comprises all qualified CRs with available public…

EPDnew
Dataset

EPDnew

A recently introduced new part of the Eukaryotic Promoter Database (EPD) which…

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…

DPTF
Dataset

DPTF Database of Poplar Transcription Factors

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…

RegPrecise
Dataset

RegPrecise

A database for capturing, visualization and analysis of transcription factor…

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.

LegumeTFDB
Dataset

LegumeTFDB

A public database that provides predicted transcription factor (TF) encoding…

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…

P2CS
Dataset

P2CS

A comprehensive resource for the analysis of Prokaryotic Two-Component Systems…

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…

STIFDB
Dataset

STIFDB Stress Responsive Transcription Factor Database

A comprehensive collection of biotic and abiotic stress responsive genes in…

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…

Pigeonpea…
Dataset

Pigeonpea Transcription Factors Database

Provides a range of information about the pigeonpea transcription factors (TFs)…

Provides a range of information about the pigeonpea transcription factors (TFs) for public domain. PpTFDB is searchable by TF categories that facilitates user to browse available transcription…

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TMREC
Dataset

TMREC Transcription factor and MiRNA Regulatory Cascades in Human Diseases

A database which provides a user-friendly interface for convenient retrieval…

A database which provides a user-friendly interface for convenient retrieval and visualization of TF-miRNA regulatory cascades and clusters in specific disease by TF, miRNA or disease name. TMREC…

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SlideBase
Dataset

SlideBase

Offers a way of selecting genes, promoters, enhancers and microRNAs that are…

Offers a way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. SlideBase…

PvTFDB
Dataset

PvTFDB Phaseolus vulgaris transcription factors database

The first online comprehensive transcription factors (TF) database developed…

The first online comprehensive transcription factors (TF) database developed for the legume crop Phaseolus vulgaris L. (Common Bean). PvTFDB contains a set of 2370 predicted TFs (Gene models) and…

TOBFAC
Dataset

TOBFAC

It came into being as a database of tobacco transcription factors at the time,…

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).

SM-TF
Dataset

SM-TF Small Molecule-Transcription Factor

A structural database of small molecule-transcription factor complexes. The 3D…

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…

Transcompel
Dataset

Transcompel

A database on composite elements. TRANSCompel focuses on so-called composite…

A database on composite elements. TRANSCompel focuses on so-called composite elements, consisting of two (or more) neighboring binding sites, characterized by synergistic or antagonistic effects…

CollecTF
Dataset

CollecTF

Compiles data on experimentally validated, naturally occurring transcription…

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…

OnTheFly
Dataset

OnTheFly

A systematic determination of Drosophila melanogaster transcription factor…

A systematic determination of Drosophila melanogaster transcription factor DNA-binding specificities.

mTFkb
Dataset

mTFkb mouse Transcription Factor knowledgebase

Provides expression data, functional analysis results as well as functional…

Provides expression data, functional analysis results as well as functional annotations of 33 major mouse tissues. mTFkb permits to inspect the expression profile and analysis results for each mouse…

Cistrome DB
Web

Cistrome DB Cistrome Data Browser

A collection of ChIP-seq and chromatin accessibility data (DNase-seq and…

A collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) including 13366 human and 9953 mouse samples. Cistrome DB contains data which have been carefully curated and…

FASTFORWARD DNA
Dataset

FASTFORWARD DNA

A text-mining-assisted workflow to systematically extract knowledge about…

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,…

DATFAP
Dataset
PlantTFcat
Dataset

PlantTFcat

A web-based analysis tool that is designed to identify and categorize plant…

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…

TFCat
Dataset

TFCat

A curated catalog of mouse and human transcription factors (TF) based on a…

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…

CardioTF
Dataset

CardioTF

Captures all transcriptional information relating to cardiovascular…

Captures all transcriptional information relating to cardiovascular development. CardioTF is used to collate information on cardiovascular transcription factors (TFs), position weight matrices…

YTRP
Dataset

YTRP Yeast Transcriptional Regulatory Pathway

Database for yeast biologists with these comprehensive transcriptional…

Database for yeast biologists with these comprehensive transcriptional regulatory pathway (TRP) information and the accompanying literature supports for the TRPs.

TrSDB
Dataset

TrSDB

A proteome database of eukaryotic transcription factors based upon predicted…

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…

HemoPDB
Dataset

HemoPDB Hematopoiesis Promoter Database

A comprehensive resource focused on transcriptional regulation during…

A comprehensive resource focused on transcriptional regulation during hematopoietic development and associated aberrances that result in malignancy.

REGULATOR
Dataset

REGULATOR

A metazoan transcription factor and maternal factor resource specially designed…

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…

TFinDIT
Dataset

TFinDIT Transcription Factor-DNA Interaction Data deposITory

A relational database and a web search tool for studying transcription…

A relational database and a web search tool for studying transcription factor-DNA interactions. The database contains annotated transcription factor-DNA complex structures and related data, such as…

RiceSRTFDB
Dataset

RiceSRTFDB Rice Stress-Responsive Transcription Factor Database

Provides access to cis-regulatory elements and mutant information for rice…

Provides access to cis-regulatory elements and mutant information for rice transcription factors (TFs). RiceSRTFDB is a user-friendly web interface that also offers access to the expression profiles…

GraP
Dataset

GraP Platform of Functional genomics analysis in Gossypium raimondii

Provides an integration, multi-dimensional analysis and visualization platform…

Provides an integration, multi-dimensional analysis and visualization platform for cotton functional genomics research. GraP includes updated functional annotation, gene family classifications,…

TFcheckpoint
Dataset

TFcheckpoint Transcription Factor Checkpoint

Provides a high-quality and comprehensive knowledge source for genome-scale…

Provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies. TFcheckpoint is an exhaustive collection of TFs annotated according to experimental and other…

CardioSignal
Dataset

CardioSignal

Provides online analysis tools to speeding up hypothesis-driven research in…

Provides online analysis tools to speeding up hypothesis-driven research in gene regulation. CardioSignal was designed for integration of regulatory information on the transcriptional regulation…

wDBTF
Dataset

wDBTF Database of Wheat Transcription Factor

Compiles a classified list of wheat transcription factors (TF) sequences…

Compiles a classified list of wheat transcription factors (TF) sequences validated by the presence of a DNA-binding domain out. The TF family names link to individual TF family or subfamily pages.…

P2RP
Web

P2RP Predicted Prokaryotic Regulatory Proteins

Enables users to identify and annotate transcription factors (TFs) and…

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…

P2TF
Dataset

P2TF Predicted Prokaryotic Transcription Factors

An integrated and comprehensive database relating to transcription factor…

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…

CarrotDB
Web

CarrotDB

A Web-based genomic and transcriptomic database for D. carota. It offers the…

A Web-based genomic and transcriptomic database for D. carota. It offers the tools of Genome Map and Basic Local Alignment Search Tool.

iTAK
Desktop
Web

iTAK

A program to identify plant transcription factors (TFs), transcriptional…

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…

AtProbe
Dataset

AtProbe

Focuses on specific binding elements on known genes, found with experimental…

Focuses on specific binding elements on known genes, found with experimental methods.

SwissRegulon
Dataset

SwissRegulon

The database contains genome-wide annotations of regulatory sites.

The database contains genome-wide annotations of regulatory sites.

YEASTRACT
Dataset

YEASTRACT Yeast Search for Transcriptional Regulators And Consensus Tracking

A curated repository of more than 206000 regulatory associations between…

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.

hmChIP
Dataset

hmChIP

A database of genome-wide chromatin immunoprecipitation (ChIP) data in human…

A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse.

PAZAR
Dataset

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.

Cscan
Web

Cscan

A web resource that includes a large collection of genome-wide ChIP-Seq…

A web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others.

ENCODE
Dataset

ENCODE

The goal is to build a comprehensive parts list of functional elements in the…

The goal is to build a comprehensive parts list of functional elements in the human genome.

MPromDb
Dataset

MPromDb Mammalian Promoter Database

Integrates gene promoters with experimentally supported annotation of…

Integrates gene promoters with experimentally supported annotation of transcription start sites, cis-regulatory elements, CpG islands and chromatin immunoprecipitation microarray (ChIP-chip)…

FlyTF
Dataset

FlyTF Transcription factor datamine for Drosophila melanogaster

Collects information about transcription factors (TFs) in the fruit fly…

Collects information about transcription factors (TFs) in the fruit fly Drosophila melanogaster. FlyTF provides results from the curation of over 1052 candidate TFs selected for the presence of a…

Tractor_DB
Dataset

Tractor_DB

Contains a collection of computationally predicted Transcription Factors'…

Contains a collection of computationally predicted Transcription Factors' binding sites in gamma-proteobacterial genomes.

ProTISA
Dataset

ProTISA

Intended to collect confirmed translation initiation sites (TISs) for…

Intended to collect confirmed translation initiation sites (TISs) for prokaryotic genomes.

SoyDB
Dataset

SoyDB

A knowledge database for all the transcription factors in the soybean genome.…

A knowledge database for all the transcription factors in the soybean genome. SoyDB contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous…

TreeTFDB
Dataset

TreeTFDB

Provides the complete transcription factor (TF) repertoires of 6 genome…

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.

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DPRP
Dataset

DPRP Database of Phenotype-specific Regulatory Programs

Facilitates the search and application of gene expression data for generating…

Facilitates the search and application of gene expression data for generating new hypotheses on transcriptional regulatory programs under diverse biological and clinical contexts. DPRP contains about…

Targetfinder.or…
Web

Targetfinder.org

Provides a web-based resource for finding genes that show a similar expression…

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…

COMPEL
Dataset

COMPEL

A database on composite regulatory elements, the basic structures of…

A database on composite regulatory elements, the basic structures of combinatorial regulation. Composite regulatory elements contain two closely situated binding sites for distinct transcription…

ITFP
Dataset

ITFP Integrated Transcription Factor Platform

An integrated transcription factor (TF) platform that included abundant TFs and…

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…

NPEST
Dataset

NPEST

A tool for the analysis of expressed sequence tags (EST) distributions and…

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…

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