TRP - Transcriptional Portal : Listed by Species

Listed by Species

Animal
TarBase

Arabidopsis thaliana
PhosPhAt

PlantTribes

RARTF - RIKEN Arabidopsis Transcription Factor database

The Arabidopsis Information Resource

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.

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.

ASRP

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

AthaMap

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

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.

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.

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.

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.

DATF - Database of Arabidopsis Transcription Factors

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

NASCArrays - Nottingham Arabidopsis Stock Centre's microarray database

PRI-CAT

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

Archaea
TraP - Transcription Product Database

SGCRGES - Structural Genomics Consortium for Research on Gene Expression System

ExtraTrain

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

TTDB - Transcription-Translation DataBase

B. subtilis
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.

Bacillus
SuperCAT

Bacteria
SGCRGES - Structural Genomics Consortium for Research on Gene Expression System

VFDB

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

ExtraTrain

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

TTDB - Transcription-Translation DataBase

Black cottonwood tree
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.

C.elegans
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.

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.

Chicken
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.

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.

Chimpanzee
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.

Chordata
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.

Cyanobacteria
cTFbase

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

Drosophila
CDMC - Canadian Drosophila microarray centre

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

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.

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.

REDfly 2.0

TFDBS

FlyFactorSurvey is a database of Drosophila TFs DNA binding specificities.

NATsDB

E.coli
PromEC - Database of E.coli mRNA promoters

RegulonDB - Escherichia coli K12 Transcriptional Network

Tractor db - Regulatory networks in gamma-proteobacteria

Bacteriome.org

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

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.

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.

ECDC - E.coli database collection

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

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.

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.

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.

Eukaryote
TTDB - Transcription-Translation DataBase

TRANSFAC - Eukaryotic Transcription Factor Database

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.

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.

NATsDB

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

Human
mtSNP - human mitochondrial genome single nucleotide polymorphism database

ncRNA

OPD - Osteo-Promoter Database

OPHID - The Online Predicted Human Interaction Database

PEDB - Prostate Expression Databases

PReMod

RefExA - Reference database for Expression Analysis

SIEGE - Smoking Induced Epithelial Gene Expression

TiProD

ARED Organism

AU-RICH ELEMENT-CONTAINING mRNA DATABASE

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.

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.

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.

Evola

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

Factorbook

Human transcription factor-binding data from ChIP-seq.

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.

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.

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.

HOCOMOCO

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

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.

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.

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.

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.

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.

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.

MethyCancer

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.

MutDB

PepCyber:PPEP

SelenoDB 1.0

SNPeffect

TFClass

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

The cell cycle DB

The H-Invitational Database

The vertebrate genome annotation database

Vir-Mir db

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

GenomeTraFaC

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

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.

NATsDB

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.

PromoSer

SOURCE - Unification Tool to Navigate GeneReports

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.

Transcription Factors database

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.

Maize
Panzea

Gramene

Gramene is A Resource for Comparative Grass Genomics.

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.

Mammal
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.

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.

Medaka
MEPD - A medaka gene expression pattern database

UTGB/medaka

UTGB is browser for medaka genome.

Mouse
GenomeTraFaC

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

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.

NATsDB

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.

PromoSer

SOURCE - Unification Tool to Navigate GeneReports

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.

Mouse SAGE Site - Mouse Serial Analysis of gene expression Site

MUGEN mouse database

Pbmice

TFDB - Riken Transcription Factor Database

CAGE - Cap Analysis of Gene Expression

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

GenePaint.org

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

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.

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.

Multiple
MegaMotifBase

MEROPS

MetaCrop

miRBase

miRGator

Mitome

MPromDb - Mammalian Promoter Database

MSY Breakpoint Mapper

Narcisse

NBRP - National BioResource Project

NCBI - National Center for Biotechnology Information

NetworKIN

NONCODE v2.0

NORINE

ODB - Operon Database

ooTFD - object-oriented Transcription Factors Database

OPTIC

ORegAnno - Open REGulatory ANNOtation database

ORF Browser

OrthoDB

PairsDB

PANDIT-Protein and Associated Nucleotide Domains with Inferred Trees

PEPR - Public Expression Profiling Resource

PHI-base update

Phospho.ELM

PhylomeDB

piRNABank

PlantGDB

PlantProm - Plant promoter sequences

PlantTFDB

ppdb

PPT-DB

PRIDE

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

PROCOGNATE

PRODORIC - Prokaryotic Database of gene Regulation

ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions

ProSAS

PROSITE - Database of protein families and domains

ProTISA

ProtozoaDB

PubMeth

QuadBase

R.E.DD.B.

Resource Center for Biodefense Proteomics Research

Rfam

RNA FRABASE version 1.0

RNAJunction

SAGEmap - Serial Analysis of Gene Expression Tag to Gene Mapping

Shanghai RAPESEED Database

SIMAP

SMD - Stanford MicroArray Database

SmedGD

StellaBase

STITCH

SuperTarget and Matador

TargetDB

TESS - Transcription Element Search System

TFFACTOR

The 3D rRNA modification maps database

The BioGRID Interaction Database

The Gene Ontology

The Generation Challenge Programme

The Genomes On Line Database

The Gypsy Database of mobile genetic elements

The HGNC Database

The integrated microbial genomes

The ITS2 Database II

The MetaCyc

The microRNA.org resource

The Molecule Pages database

The pharmacogenetics and pharmacogenomics knowledge base

The Plant Ontology Database

The plant organelles database

The Rice Annotation Project Database

The Stanford Tissue Microarray Database

The Telomerase Database

The UCSC Genome Browser Database

The UniTrap

TRANSCompel - Database on Composite Regulatory Elements affecting Gene Transcription

TranspoGene and microTranspoGene

Transterm - Database of mRNA sequences and regulatory elements

TRED - Transcriptional Regulatory Element Database

TreeFam

TRRD - Transcription Regulatory Regions Database

TrSDB

UgMicroSatdb

UMD - UNC Microarray Database

Arabidopsis Next-Gen Sequence DBs

Arabidopsis next-generation sequence databases

AutoPSI

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

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.

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.

CFGP

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

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.

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.

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.

Cyclebase.org

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

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 .

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.

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.

EndoNet

EndoNet is a database that provides information about endocrine networks.

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.

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.

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.

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.

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.

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.

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.

Greglist

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

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.

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.

JASPAR - The high-quality transcription factor binding profile database

JASPAR is the high-quality transcription factor binding profile database

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.

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.

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.

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.

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.

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.

X:Map

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

Other organisms
Transcription Factors database

Plant
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.

Gramene

Gramene is A Resource for Comparative Grass Genomics.

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.

PlantCARE

PLEXdb

PLACE

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

PlnTFDB

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

TarBase

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.

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.

Prokaryotes
PRODORIC

RegTransBase

SwissRegulon

Rat
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.

PromoSer

SOURCE - Unification Tool to Navigate GeneReports

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.

MGI - Mouse Genome Informatics

Ratmap - The Rat Genome Database

RGD - Rat Genome Database

rOGED - Rat Ovarian Gene Expression Database

Rice
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.

DRTF - Database of Rice Transcription Factors

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

OikoBase

Genome expression database of Oikopleura dioica.

Oryza Tag Line

RiceFREND

Rice Functionally Related gene Expression Network Database.

RiceTFDB

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).

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.

Saccharomyces cerevisiae
S.pombe - The Schizosaccaromyces pombe Genome Project

SCPD - The Promoter Database of Saccharomyces cerevisiae

SGD - Saccharomyces Genome Database

TransfactomeDB

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.

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.

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.

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.

Sorghum
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.

Sugarcane
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.

Tunicates
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.

Vertebrate
miRNAMap

ECRbase

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

Virus
The hepatitis C sequence database

Worm
ToxoDB

Xenopus laevis
Xenbase

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

Zebrafish
The Zebrafish Information Network

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.

rat
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.