TRP - Transcriptional Portal : Listed by Category

Listed by Category

Binding Sites
PathoDB

PathoDB provides data on pathologically relevant mutated forms of transcription factors and their binding sites.

PredictRegulon

PredictRegulon is a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes.

TFDBS

FlyFactorSurvey is a database of Drosophila TFs DNA binding specificities.

rSNP_Tools

Prediction of TF-sites damaged/appeared due to SNP.

Cancer
CGED - Cancer Gene Expression Database

CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information and includes data on breast (prognosis and docetaxel data sets), colorectal, hepatocellular, esophageal, thyroid, and gastric cancers.

ChIP-chip data
CEAS

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

Factorbook

Human transcription factor-binding data from ChIP-seq.

HRTBLDb

Horomone Receptor Target Binding Loci Database (HRTBLDb). Data from high through-put lab techniques (ChIP-chip, ChIP-Seq, and ChIP-PET) are integrated in to this unified database to aid research on the hormone signaling pathways that regulate gene expression.

PRI-CAT

PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis.

Cis-regulatory elements
CisMols

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

POBO

POBO, transcription factor binding site verification with bootstrapping. POBO is a tool to summarize, verify and screen predetermined cis-elements from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

POXO

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes. Hosts tools-POBO, POCO, GENERATOR, VISUALIZE, TRACKER, SCREENER, MATLIGN, DANCER

Tracker

Tracker is a tool for evolutionary footprinting. It can be used to visualize potential cis-elements within the analyzed sequences and within their homologous sequences in other organisms. After finding the regulatory patterns, another approach for their evaluation is to look for their locations in the corresponding homologous sequences.

Fish
GENSAT - Gene Expression Nervous System Atlas

The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques.

Gene expression
ACT

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

Athena

Athena is a web-based application that warehouses disparate datatypes related to the control of gene expression. Provide: Transcription factor binding site enrichment tool to identify statistically over-represented TF sites occurring in a selected set of promoters.

BioProspector

BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs.

CellLineNavigator

The CellLineNavigator database is a web-based workbench for large scale comparisons of a vast amount of diverse cell lines to support experimental design in the fields of genomics, systems biology and translational biomedical research. It allows the user to explore and filter the gene expression focusing on pathological or physiological conditions.

DANCER

Dancer is a stand-alone tool that runs in Windows operating system. Dancer can be used to reconstruct in-situ hybridization pictures from gene expression data.

FFGED

The Filamentous Fungal Gene Expression Database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results.

GeneMania

GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity.

Generator

Generator is a tool to evaluate and group incoherently annotated genes into subsets according to their gene ontology (GO) terms. After the set of co-expressed genes has been gathered, the functions of the genes can be examined.

HOXPro

Homeobox Genes Data Base. This database contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes.

HemaExplorer

HemaExplorer provides a plot of gene expression in hematopoietic cells at different maturation stages based on curated microarray data.

MIRAGE

MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression) is a web resource of the Institute for Transcriptional Informatics, dedicated to methodologies, tools, and technologies relating to gene expression information.Tools: ooTFD, Tfsitescan, Tfdaa.

OikoBase

Genome expression database of Oikopleura dioica.

POCO

POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. POCO is tool to find over-represented, under-represented and distinctly represented regulatory patterns from either one or two sequence sets.

RiceFREND

Rice Functionally Related gene Expression Network Database.

VAMPIRE

VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.

YPA

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene expression data) and provides a comprehensive view of the promoter regions.

ZiFiT

The ZiFiT Targeter software package is designed to aid research in the application of gene editing and expression technologies.

rSNP_DB

Database on magnitudes characterizing the influence of single nucleotide mutations in regulatory gene regions onto their interaction with nuclear proteins.

visANT

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data.

Gene regulation
ARGO

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

CPDB

ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways.

Cluster Buster

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences. The main application is detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too.

CompareProspector

Server which attempts to identify any motifs related to genes predicted to share regulatory elements.

DroID

DroID is a comprehensive gene and protein interactions (interactome) database designed specifically for the model organism Drosophila. The database now includes transcription factor-gene and regulatory RNA-gene interactions.

HLungDB

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

NXSensor

Nucleosome eXclusion Sensor (NXSensor) is a tool for finding regions of DNA sequences that are likely to be nucleosome-free. NXSensor should be a useful tool in assessing the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.

PLACE

PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports.

RSAT

Regulatory Sequence Analysis Tools (RSAT). This web site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.

Screener

Screener is a tool to associate the patterns found to known elements listed in cis-element collection. After finding the patterns with a potential regulatory role, patterns can be evaluated by screening for resembling cis-elements from the known cis-element collections. In pattern screener, the found patterns can be screened against PLACE, JASPAR or TRANSFAC public.

SynoR

SynoR searches vertebrate genomes for synonymous regulatory elements.

UCNEbase

Ultraconserved non-coding elements and gene regulatory blocks. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes.

Visualize

Visualize is a tool to visualize the locations of regulatory patterns within the sequences.

mirConnX

Condition-specific mRNA-microRNA network integrator. mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks.

rSNP_BIB

Database on references describing the influence of single nucleotide mutations in regulatory gene regions onto their interaction with nuclear proteins.

rSNP_Guide

A system of databases documenting the influence of mutations in regulatory gene regions. Databases: rSNP_DB, rSNP_BIB, MATRIX, SAMPLES, SYSTEM. Tools: rSNP_Tools.

Genes and Diseases
ORF Browser

mtSNP - human mitochondrial genome single nucleotide polymorphism database

Genomics
Babelomics

Babelomics is an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.

Colibri - Analysis of the Genome of E.coli

Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments.

DECODE

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

DPTF - a database of poplar transcription factors.

The Database of Poplar Transcription Factors (DPTF) collected known and predicted transcription factors (TF) of the black cottonwood tree, Populus trichocarpa.

Dire

A web server developed from Distant Regulatory Elements, based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant REs in higher eukaryotic genomes.

EchoBASE - an integrated post-genomic database for E.coli

EchoBASE is a database that has been created to integrate information from post-genomic experiments into a single resource with the aim of then providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function.

EcoCyc - Encyclopedia of Escherichia coli K-12 Genes and Metabolism

EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

ExtraTrain

ExtraTrain is a database for exploring Extragenic space and Transcriptional information in bacteria and archaea.

GRSDB

‘G’-Rich Sequences DataBase contains information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the alternatively processed (alternatively spliced or alternatively polyadenylated) mammalian pre-mRNA sequences.

GeneDB

GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation.

GenoBase - Genome Analysis Project in Japan

GenoBase is the public repository for Sequence Information, Proteome, Transcriptome, Bioinformatics, and Knowledge based on literature concerning E.coli.

Genome Surveyor

Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.

GenomeTraFaC

A comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs.

HGVbase - Human Genome Variation Database

The objective of HGVbase (the Human Genome Variation Database) is to provide an accurate, high utility and ultimately fully comprehensive catalog of normal human gene and genome variation, useful as a research tool to help define the genetic component of human phenotypic variation.

MGI - Mouse Genome Informatics

NATsDB

PReMod

PlnTFDB

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

RARTF - RIKEN Arabidopsis Transcription Factor database

RGD - Rat Genome Database

Ratmap - The Rat Genome Database

RiceTFDB

S.pombe - The Schizosaccaromyces pombe Genome Project

SGD - Saccharomyces Genome Database

TTDB - Transcription-Translation DataBase

TraP - Transcription Product Database

cTFbase

The cTFbase was created to store and analyze all the putative transcription factors (TFs) in the cyanobacterial genomes.

miRNAMap

Integration
CCDB - The CyberCell Database

The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli.

ECDC - E.coli database collection

This collection offers you all information regarding the entire E.coli K12 chromosome.

NBRP - National BioResource Project

NCBI - National Center for Biotechnology Information

SCPD - The Promoter Database of Saccharomyces cerevisiae

TRANSFAC - Eukaryotic Transcription Factor Database

Interactions
HPRD - Human Protein Reference Database

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.

OPD - Osteo-Promoter Database

ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions

RegTransBase

TcoF

Dragon database of transcription co-factors and transcription factor interacting proteins.

Matrices
Matlign

Matlign (Matrix alignment) is a tool to align and combine a set of nucleotide matrices and/or patterns onto a smaller and more representative set of nucleotide matrices and/or patterns. The tool was originally developed for the analyses of transcription factor binding site matrices/patterns, and was therfore designed to create only a certain maximum number of gaps on the alignment.

MatrixCatch

The MatrixCatch algorithm searches for potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence.

P-Match

P-Match is a program for predicting transcription factor binding sites (TFBS) in DNA sequences that combines pattern matching and weight matrix approaches.

T-Reg Comparator

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).

TFM-CUDA

TFM-CUDA is a CUDA implementation of parallel algorithms able to: scan a matrix or a set of matrices against a sequence (see also TFM-Scan), compute the P-value corresponding to a score, or the score corresponding to a Pvalue.

Microarray Data and Gene Expression
CAGE - Cap Analysis of Gene Expression

The database for transcript which analysised by Cap Analysis Gene Expression in mouse.

CATMA - A Complete Arabidopsis Transcriptome MicroArray

The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.

CDMC - Canadian Drosophila microarray centre

The CDMC is a microarray facility for Canadian and international academic scientists working with Drosophila.

GEO - Gene Expression Omnibus

Gene Expression Omnibus: a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted.

GPXdb - Macrophage Expression Atlas

Macrophage Expression Atlas is a database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.

GenePaint.org

GenePaint.org is a digital atlas of gene expression patterns in the mouse.

GeneTide - Terra Incognita Discovery Endeavor

GeneTide is an automated system for annotation of human transcripts - mRNA and ESTs, and the eulcidation of de-novo genes.

GermOnline - Knowledgebase of microarray data

The GermOnline gateway is a cross-species microarray expression database focusing on germline development, meiosis and gametogenesis as well as the mitotic cell cycle.

HPMR - Human Plasma Membrane Receptome

Users can search for ligand or receptor to reveal plasma membrane receptors pairing partners and browse through ligand or receptor families to identify ligand-receptor relationships.

HUVEC DB - Human Umbilical Vein Endothelial Cells Database

HUVEC (human umbilical vein endothelial cells) database shows the expression pattern of HUVEC which treated with several agonists.

HemoPDB - Hematopoiesis Promoter Database

The Hematopoiesis Promoter Database (HemoPDB) has been developed as a publicly available, web-based information resource focused on transcriptional regulation in hematopoiesis.

HugeIndex - Human Gene Expression Index

The mRNA expression levels of thousands of genes in a collection of normal human organs were obtained using high-density oligonucleotide array technology and deposited in this public database.

ITTACA - Integrated Tumor Transcriptome Array and Clinical data Analysis

ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma.

MAMEP - Molecular Anatomy of the Mouse Embryo Project

The project is aiming to create a comprehensive information resource for the functional analysis of pattern formation, tissue development and organogenesis.

MEPD - A medaka gene expression pattern database

Mouse SAGE Site - Mouse Serial Analysis of gene expression Site

NASCArrays - Nottingham Arabidopsis Stock Centre's microarray database

PEDB - Prostate Expression Databases

PEPR - Public Expression Profiling Resource

PLEXdb

RefExA - Reference database for Expression Analysis

RiceXPro

The Rice Expression Profile Database (RiceXPro) is a repository of gene expression profiles derived from microarray analysis of tissues/organs encompassing the entire growth of the rice plant under natural field conditions, rice seedlings treated with various phytohormones, and specific cell types/tissues isolated by laser microdissection (LMD).

SAGEmap - Serial Analysis of Gene Expression Tag to Gene Mapping

SIEGE - Smoking Induced Epithelial Gene Expression

SMD - Stanford MicroArray Database

SOURCE - Unification Tool to Navigate GeneReports

TRIPLES - a databases of Transposon-Insertion Phenotypes Localization and Expression in Saccharomyces

UMD - UNC Microarray Database

dbERGE II - Database of Experimental Results on Gene Expression

dbERGE II stores experiment and result details for various types of experiments: DNA transfer experiments (Transfections and Transgenic mice), Binding assays (Gel shift, In-vivo footprint, In-vitro footprint and Methylation interference), Hypersensitive sites and ChIP - on - chip experiments.

rOGED - Rat Ovarian Gene Expression Database

yMGV - yeast Microarray Global Viewer

The Yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of yeast genes among most of the published expression datasets.

Motifs
MotifViz

Motif Search and Visualization. MotifViz is a tool for detecting overrepresented transcription factor binding motifs.

modtools

Tools for MOtif Discovery in nucleotide sequences Cscan, PScan, Weeder, WeederH.

Network
ATTED-II

ATTED-II provides co-regulated gene relationships to estimate gene functions in Arabidopsis thaliana.

AtTFDB

AtTFDB is a comprehensive and public Arabidopsis transcription factor database.

OPHID - The Online Predicted Human Interaction Database

PRODORIC

RegulonDB - Escherichia coli K12 Transcriptional Network

Nucleotide Sequence
AGRIS - Arabidopsis Gene Regulatory Information Server

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains three databases.

DATF - Database of Arabidopsis Transcription Factors

The Database of Arabidopsis Transcription Factors (DATF) collects all arabidopsis transcription factors and classifies them into 64 families.

DBD - Transcription factor prediction database

The DBD (www.transcriptionfactor.org) consists of predicted transcription factor repertoires for 150 completely sequenced genomes, their domain assignments and the hand curated list of DNA-binding domain hidden Markov models.

DBTSS - DataBase of Transcriptional Start Sites

DBTSS represents exact positions of transcriptional start sites (TSSs) in the genome based on cDNA sequence of human, mouse, zebrafish, malaria, C. merolae, rattus,chimpanzee, and M. fascicularis .

DRTF - Database of Rice Transcription Factors

The Database of Rice Transcription Factors (DRTF) is a collection of known and predicted transcription factors of rice.

DoOP - Databases of Orthologous Promoters

DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species.

EPD - The Eukaryotic Promoter Database

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.

GeneNet

The GeneNet system integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description.

JASPAR - The high-quality transcription factor binding profile database

JASPAR is the high-quality transcription factor binding profile database

MAPPER - Multi-genome Analysis of Positions and Pattern of elements of Regulation

MAPPER is a platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes.

MPromDb - Mammalian Promoter Database

ODB - Operon Database

PRODORIC - Prokaryotic Database of gene Regulation

PlantProm - Plant promoter sequences

PromEC - Database of E.coli mRNA promoters

PromoSer

Rfam

TESS - Transcription Element Search System

TRANSCompel - Database on Composite Regulatory Elements affecting Gene Transcription

TRED - Transcriptional Regulatory Element Database

TRRD - Transcription Regulatory Regions Database

Tractor db - Regulatory networks in gamma-proteobacteria

Transterm - Database of mRNA sequences and regulatory elements

YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.

cisRED - cis/computational/in silico Regulatory Element Database

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations.

ooTFD - object-oriented Transcription Factors Database

Prediction for DNA-Binding and Binding Sites
ABS

ABS is a public database of experimentally verified orthologous transcription factor binding sites (TFBSs). Annotations have been collected from the literature and are manually curated. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken.

DBTBS

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

DBTGR - DataBase of Tunicate Gene Regulation

DBTGR provides information on tunicate gene regulation such as the location of expression, or the identified regulatory elements present in promoter sequences.

ECRbase

ECRbase is the Database of Evolutionary Conserved Regions (ECRs), Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes created using ECR Browser alignments.

Escherichia coli Transcription Factor Binding Sites

This site presents transcription factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding.

GRASSIUS

GRASSIUS 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.

ORegAnno - Open REGulatory ANNOtation database

PlantCARE

ReadOUT - Calculations of Specificities and energies for Protein-DNA complexes

This server calculates: (1) The DNA conformational energy and Z-score, and (2) The direct readout or base-amino acid interaction energy and Z-score for protein-DNA complex structures. This server may be useful if you want to check the specificity of particular protein-DNA complex.

SwissRegulon

TFDB - Riken Transcription Factor Database

TFFACTOR

TarBase

Transcription Factors database

ncRNA

Promoters
TiProD

Protein Structure and Domains
PANDIT-Protein and Associated Nucleotide Domains with Inferred Trees

PDBnet - Bird's-eye View of Molecular Network in the Structurome

PDBnet provides a bird's-eye view of molecular organization in the structurome, and enable users to extract various kinds of information about structures, interactions and networks of biomolecules. The network includes gene regulatory network.

PROSITE - Database of protein families and domains

SGCRGES - Structural Genomics Consortium for Research on Gene Expression System

TargetDB

TrSDB

Transcription factors
AliBaba

AliBaba is a program, developed by Niels Grabe, for predicting binding sites of transcription factor binding sites in an unknown DNA sequence using binding sites from TRANSFAC Public.

AthaMap

AthaMap provides a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana.

CONREAL

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

CRSD

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

CentDist

CENTDIST is a co-motif scanning program to identify co-transcription factors.

ChIP-Array

ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.

Chinook

The ORC web application is powered by Chinook to provide competing assessments of tools involved in transcription factor binding site discovery.

CisRegTest

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.

Composite Module Analyst (CMA)

Defining promoter models based on the composition of transcription factor binding sites and their pairs.

Consite

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

CoryneRegNet

Database and Analysis platform for corynebacterial transcription factors and gene regulatory networks.

Cscan

cscan is a web server finding transcription factors regulating a set of genes using binding data from a large collection of ChIP-Seq experiments in human and mouse.

Drosophila DNase I Footprint Database

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

F-Match

F-Match is a program for identifying statistically over-represented transcription factor binding sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency.

FlyTF

This database contains information on the manual curation of 1052 FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database.

Footer

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

HOCOMOCO

HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor-binding site models.

ITFP

ITFP is an integrated platform of mammalian transcription factors.

MATRIX

Database on weight matrices of the transcription factor binding sites.

MONKEY

MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.

Match

Match is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences.

Matinspector

Hosts predicting transcription factor binding sites tools such as Match, F-Match, Patch, P-Match,AliBaba2, molwSearch, MatrixCatch, SbBlast, SignalScan, TfBlast.

MycoRegNet

Database of Mycobacterial Transciption Factors and Regulatory Networks.

PROMO

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest.

PTM-Switchboard

PTM-Switchboard is designed to catalog known cases of TF-PTMs affecting gene transcriptions.

Patch

Patch is a pattern-based program for predicting transcription factor binding sites (TFBS) in DNA sequences.

PromoterPlot

PromoterPlot is an interactive viewer of transcription factor binding sites on promoters and a tool to uncover common transcription factor binding patterns.

ProteDNA

Predictor of sequence-specific DNA-binding residues in transcription factors.

Pscan

Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.

REDUCE

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly.

RegPrecise

The RegPrecise is 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.

SAMPLES

A database of regulatory active genomic regions. Investigation of transcriptional factors binding sites of eukaryotes.

SITECON

A tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition.

SiteSeer

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

TFBScluster

This web tool is designed to identify clusters of transcription factor binding sites (TFBSs) that are conserved between mammalian genomes.

TFClass

Human transcription factors classified according to their DNA-binding domains.

TFM

Transcription Factor Matrices. TFM is a software suite from the Bonsai bioinformatics group for identifying and analyzing transcription factor binding sites in DNA sequences. Hosts: TFM-EXplorer, TFM-Scan, TFM-Pvalue, TFM-CUDA

TFM-Explorer

TFM-Explorer (Transcription Factor Matrix Explorer) is a program for analysing regulatory regions of eukaryotic genomes.

TFM-Pvalue

TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.

TFM-Scan

TFM-Scan is a program dedicated to the location of large sets of putative transcription factor binding sites on a DNA sequence.

TOUCAN

TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes.

TRANSPATH

TRANSPATH provides data about protein-protein interactions and directed modification of proteins involved in signal transduction pathways, with a particular focus on signaling cascades that affect the activity of transcription factors.

TfBlast

Search the TRANSFAC Public Factor Table by protein sequence.

TransmiR

TransmiR is a database for transcription factor-microRNA regulations.

YMF

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs.

molwSearch

Search for TRANSFAC Public transcription factors by molecular weight.

oPOSSUM

oPOSSUM is a web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

rVista

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.

Transcriptional regulation
CARRIE

Computational Ascertainment of Regulatory Relationships (Inferred from Expression). CARRIE takes two condition microarray data and applies promoter analysis to infer the stimulated/repressed transcriptional regulatory network.

ChIPBase

ChIPBase, 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 protein-coding genes from ChIP-Seq data.

LSPD

The Liver Specific Gene Promoter Database. Provide information on transcription regulatory elements. Record binding affinity and regulatory function.

Phyloscan

Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Software for locating sequence motifs in intergenic regions.

Transcriptional regulators
FANTOM

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation.

Transcripts
miRGen

miRGen is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data.

unclassified yet
4DXpress

This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.

ARED Organism

AU-RICH ELEMENT-CONTAINING mRNA DATABASE

ASRP

Arabidopsis Small RNA Project (ASRP) website provides access to data and resources from the Carrington laboratory.

Arabidopsis Next-Gen Sequence DBs

Arabidopsis next-generation sequence databases

AtPID

The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.

AutoPSI

AutoPSI is a database for automatic structural classification of protein sequences and structures.

Bacteriome.org

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

Binding MOAD

Binding MOAD's is a collection of well resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data.

CATdb

CATdb is a free resource that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform.

CFGP

The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes.

CMGSDB

The data for the nematode C. elegans was integrated from multiple sources, databases, and websites over the WWW. All of this heterogeneous data was then integrated to be represented under a common database.

CORUM

The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more.

COXPRESdb

A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein–protein interactions.

CTCFBSDB 2.0

CTCF binding site database (CTCFBSDB) is a comprehensive collection of experimentally determined and computationally predicted CTCF binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains.

CTCFBSDB2.0

CTCF binding site database (CTCFBSDB) is a comprehensive collection of experimentally determined and computationally predicted CTCF binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains.

CanGEM

Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.

ChromDB

Three types of sequences displays are included in the database: genomic-based (predominantly plant sequences); transcript-based (EST contigs or cDNAs for plants lacking a sequenced genome); and NCBI RefSeq sequences for a variety of model animal organisms. The Gene Record Page for any sequence indicates the type of sequence.

Cyclebase.org

Cyclebase is centralized, standardized resource for researchers to inspect and download cell-cycle datasets.

DOMINE

DOMINE is a database of protein domain (domain-domain) interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions.

EndoNet

EndoNet is a database that provides information about endocrine networks.

Evola

H-Invitational Database (H-InvDB), is an integrated database of human genes and transcripts.

GISSD

Group I intron sequence and structure Database (GISSD) is a specialized and comprehensive database for group I introns, focusing on integrating useful group I intron information from all available databases.

GLIDA

GLIDA haves the following features: 1) A complex information system covering biological information of the superfamily of G-protein coupled receptors (GPCRs). 2) Two starting points: Enterable either by GPCR search or ligand search. 3) Cross-searchable between GPCRs and their ligands.

GRS_UTRdb

GRS_UTRdb contains information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the untranslated regions (UTRs) of eukaryotic mRNA sequences.

Gene3D

The Gene3D database is a large collection of CATH protein domain assignments for ENSEMBL genomes and Uniprot (Universal Protein Resource; a catalog of information on proteins) sequences.

Gramene

Gramene is A Resource for Comparative Grass Genomics.

GreenPhylDB

GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on complete genomes, covering a broad taxonomy of green plants.

Greglist

Greglist ia a database listing potential G-quadruplex regulated genes.

IMG/M

The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context.

InParanoid 7

The Inparanoid program was developed at the Center for Genomics and Bioinformatics to address the need to identify orthologs.

KEGG

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

LOCATE

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

LigASite

LigASite is a gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex.

MALISAM

MALISAM is a database of pairwise, structure-based alignments for structurally analogous motifs in proteins.

MEROPS

MSY Breakpoint Mapper

MUGEN mouse database

MegaMotifBase

MetaCrop

MethyCancer

Mitome

MutDB

NONCODE v2.0

NORINE

Narcisse

NetworKIN

OPTIC

OrthoDB

Oryza Tag Line

PHI-base update

PPT-DB

PRIDE

PROCOGNATE

PairsDB

Panzea

Pbmice

PepCyber:PPEP

PhosPhAt

Phospho.ELM

PhylomeDB

PlantGDB

PlantTFDB

PlantTribes

Priorities for nucleotide trace sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

ProSAS

ProTISA

ProtozoaDB

PubMeth

QuadBase

R.E.DD.B.

REDfly 2.0

RNA FRABASE version 1.0

RNAJunction

Resource Center for Biodefense Proteomics Research

SIMAP

SNPeffect

STITCH

SelenoDB 1.0

Shanghai RAPESEED Database

SmedGD

StellaBase

SuperCAT

SuperTarget and Matador

The 3D rRNA modification maps database

The Arabidopsis Information Resource

The BioGRID Interaction Database

The Gene Ontology

The Generation Challenge Programme

The Genomes On Line Database

The Gypsy Database of mobile genetic elements

The H-Invitational Database

The HGNC Database

The ITS2 Database II

The MetaCyc

The Molecule Pages database

The Plant Ontology Database

The Rice Annotation Project Database

The Stanford Tissue Microarray Database

The Telomerase Database

The UCSC Genome Browser Database

The UniTrap

The Zebrafish Information Network

The cell cycle DB

The hepatitis C sequence database

The integrated microbial genomes

The microRNA.org resource

The pharmacogenetics and pharmacogenomics knowledge base

The plant organelles database

The vertebrate genome annotation database

ToxoDB

TransfactomeDB

TranspoGene and microTranspoGene

TreeFam

UTGB/medaka

UTGB is browser for medaka genome.

UTRome.org

The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans. The database provides detailed information on 3'UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases.

UgMicroSatdb

VFDB

VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens.

VIOLIN

Vaccine Investigation and Online Information Network (VIOLIN) is a web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety.

Vir-Mir db

Vir-Mir database, a database containing predicted viral miRNA candidate hairpins.

X:Map

Annmap is a genome browser that includes mappings between genomic features and Affymetrix microarrays.

Xenbase

Xenbaseis a Xenopus laevis and Xenopus tropicalis biology and genomics resource.

coliSNP

This is the database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. We can search the data of SNP on this web site and display the structure of protein with SNP by RasMol.

eggNOG

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines, with functional categories.

miRBase

miRGator

piRNABank

ppdb