Pathguide: the pathway resource list
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Complete Listing of All Pathguide Resources

Pathguide contains information about 662 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

If you know of a pathway resource that is not listed here, or have other questions or comments, please send us an e-mail.

News
Major new update of Pathguide August 2013
We now have information about ~550 resources!.
Visual navigation added May 2010
Click the 'Database interactions' link on the left menu to access.
Major update
All resources were recently reviewed and many new ones were added
Get the Stats
Detailed Pathguide resource statistics now available
Pathguide Published
Please cite the Pathguide Publication



Protein-Protein Interactions  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
2P2Idb - The Protein-Protein Interaction Inhibition DatabaseDetails
Free
3D-Interologs - 3D-InterologsDetails
Free
3DID - 3D interacting domainsDetails
Free
ADAN - Prediction of protein-protein interaction of modular domainsDetailsUnavailable
AHD2.0 - Arabidopsis Hormone Database 2.0Details
Free
AllFuse - Functional Associations of Proteins in Complete GenomesDetailsUnavailable
aMAZE - Protein Function and Biochemical Pathways ProjectDetailsUnavailable
ANAP - Arabidopsis Network Analysis PipelineDetails
Free
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactomeDetails
Free
AnimalTFDB - Animal Transcription Factor DatabaseDetails
Free
AntiJen - AntiJen a Kinetic, Thermodynamic and Cellular DatabaseDetails
Free
APID - Agile Protein Interactomes DataServerDetails
Free
PSI-MI
AS-ALPS - Alternative Splicing - induced ALteration of Protein StructureDetails
Free
ASD - Allosteric DatabaseDetails
Free
ASEdb - Alanine Scanning Energetics DatabaseDetails
Free
ASPD - Artificial Selected Proteins/Peptides DatabaseDetails
Free
ATDB - Animal Toxin DatabaseDetails
Free
AtPID - Arabidopsis thaliana Protein Interactome DatabaseDetails
Free
AtPIN - Arabidopsis thaliana Protein Interactome NetworkDetails
Free
Bacteriome.org - Bacterial Protein Interaction Database for Escherichia ColiDetails
Free
BIANA - Biologic Interaction and Network AnalysisDetails
Free
BID - Binding Interface DatabaseDetails
Free
BIND - Biomolecular Interaction Network DatabaseDetails
Free
PSI-MI
BioGRID - Biological General Repository for Interaction DatasetsDetails
Free
PSI-MI
BiologicalNetworks - BiologicalNetworksDetailsUnavailable
Biozon - BiozonDetails
Free
BISC - BInary SubComplex DatabaseDetails
Free
BRITE - Functional Hierarchies and Binary Relationships of Biological EntitiesDetails
Free
CA1Neuron - Pathways of the hippocampal CA1 neuronDetailsUnavailable
CADgene - Coronary Artery Disease Gene DatabaseDetails
Free
Cancer Cell Map - The Cancer Cell MapDetails
Free
BioPAX
CancerNet - Details
Free
CCSB Interactome Database - Center for Cancer Systems Biology Interactome DatabaseDetails
Free
PSI-MI
CellCircuits - CellCircuitsDetails
Free
CHD@ZJU - Coronary Heart Disease @ZJU DatabaseDetails
Free
ChemProt - ChemProtDetails
Free
CIDeR - Details
Free
SBML
comPPI - Compartmentalized Protein-Protein Interaction DatabaseDetailsAcademic
ComSim - Database of protein structures in bound (Complex) and unbound (Single) statesDetails
Free
CORNET - CORrelation NETworksDetails
Free
CORUM - Comprehensive resource of mammalian protein complexesDetails
Free
PSI-MI
COXPRESdb - Coexpressed Gene DatabaseDetails
Free
CPDB - ConsensusPathDBDetailsAcademic
PSI-MI
CSP - Cytokine Signaling Pathway DatabaseDetailsUnavailable
CTDB - Calmodulin Target DatabaseDetails
Free
CutDB - CutDB: Proteolytic Event DatabaseDetails
Free
Cyclonet - CyclonetDetails
Free
DAnCER - Disease Annotated Chromatin Epigenetics ResourceDetails
Free
DAPID - Domain Annotated Protein-protein Interaction DatabaseDetails
Free
DASMI - Distributed Annotation System for Molecular InteractionsDetails
Free
dbSNO - database of Cysteine S-NitrOsylationDetails
Free
DDIB - Database of Domain Interactions and BindingsDetailsUnavailable
DeathDomain - Death Domain DatabaseDetails
Free
DEPOD - the human DEPhOsphorylation DatabaseDetails
Free
PSI-MI
DGA - Disease and Gene AnnotationsDetails
Free
DIMA - Domain Interaction MapDetails
Free
DIP - Database of Interacting ProteinsDetailsAcademic
PSI-MI
DIPOS - Database of Interacting Proteins in Oryza SativaDetails
Free
DOMINE - Database of Protein Domain InteractionsDetails
Free
DOMINO - Domain Peptide Interactions DatabaseDetails
Free
DOMMINO - Database of MacroMolecular Interactions Details
Free
Doodle - Database of oligomerization domains from lambda experimentsDetailsUnavailable
DopaNet - DopaNetDetailsUnavailable
Dr. PIAS - Druggable Protein-protein Interaction Assessment System DetailsUnavailable
DRC - Database of Ribosomal Crosslinks Details
Free
DroID - The Drosophila Interactions DatabaseDetails
Free
DroPNet - Drosophila Protein NetworkDetails
Free
DSM - Dynamic Signaling MapsDetailsUnavailable
EciD - E. coli Interaction DatabaseDetailsUnavailable
FIMM - Functional Molecular ImmunologyDetailsUnavailable
FLIGHT - FLIGHTDetails
Free
FLOR-ID - FLOweRing Interactive DatabaseDetails
Free
Fly-DPI - Drosophila melanogaster Database of Protein InteractomesDetails
Free
FlyBase - FlyBase: a database of Drosophila Genes & GenomesDetails
Free
FlyMine - FlyMineDetails
Free
FlyNets - FlyNetsDetailsUnavailable
FlyOde - Details
Free
FPPI - Fussarium graminearum Protein-Protein Interaction DatabaseDetails
Free
FunCoup - Networks of Functional CouplingDetails
Free
FusionDB - Prokaryote Gene Fusion EventsDetailsUnavailable
GenAge - GenAge: The Ageing Gene DatabaseDetails
Free
Gene3D - Gene3DDetails
Free
GeneMANIA - GeneMANIADetails
Free
GermOnline - GermOnlineDetails
Free
GO - Gene Ontology ConsortiumDetails
Free
GPCR-PD - G protein-coupled receptors protein databaseDetailsLicense
gpDB - A Database of G-Proteins and their Interaction with GPCRsDetails
Free
GraP - Platform of Functional Genomics Analysis in Gossypium raimondiiDetails
Free
GroEL PPI - Proteins that interact with GroEL and factors that affect their releaseDetailsUnavailable
GWIDD - Genome-WIde protein Docking DatabaseDetails
Free
H-InvDB - H-InvDB: Annotated Human Gene DatabaseDetails
Free
HAPPI - Human Annotated and Predicted Protein Interactions DatabaseDetails
Free
PSI-MI
HCPIN - Human Cancer Protein Interaction NetworkDetails
Free
HCVpro - Hepatitus C Virus Protein Interaction DatabaseDetailsAcademic
HDBase - Huntington's Disease BaseDetails
Free
HDR - Homeodomain Resource DatabaseDetails
Free
HiMAP - Human Interactome MapDetailsUnavailable
HINT - High-quality Interactomes Details
Free
HINT-KB - Human INTeractome Knowledge BaseDetails
Free
HIPPIE - Human Integrated Protein-Protein Interaction rEferenceDetails
Free
PSI-MI
HitPredict - HitPredictDetails
Free
PSI-MI
HIV-1 at NCBI - HIV-1, Human Protein Interaction Database at NCBIDetails
Free
HIVMID - HIV Molecular Immunology DatabaseDetails
Free
HomoMINT - Human Molecular Interaction DatabaseDetails
Free
PSI-MI
HotRegion - A Database of Cooperative HotspotsDetails
Free
HotSprint - Database of Computational Hot Spots of Protein InterfacesDetails
Free
HP-DPI - Helicobacter pylori Database of Protein InteractomesDetails
Free
HPID - Human Protein Interaction DatabaseDetails
Free
HPIDB - Host-Pathogen Interaction DatabaseDetails
Free
PSI-MI
HPRD - Human Protein Reference Database DetailsAcademic
PSI-MI
HSV1 PPI - Protein-Protein Interactions Table for Human herpesvirus 1DetailsUnavailable
HTRIdb - Human Transcriptional Regulation Interaction DatabaseDetails
Free
Human Proteinpedia - Human ProteinpediaDetails
Free
Human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactionsDetails
Free
HumanPSD - Human Proteome Survey Database DetailsLicense
HuPI - database of the Human Proteotheque InitiativeDetails
Free
I2D - Interologous Interaction DatabaseDetailsAcademic
PSI-MI
IBIS - Inferred Biomolecular Interactions ServerDetails
Free
ICBS - Inter-Chain Beta-SheetsDetails
Free
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and LiteratureDetails
Free
IID - Integrated Interactions DatabaseDetailsAcademic
IMEx - The International Molecular Exchange ConsortiumDetails
Free
PSI-MI
IMID - Integrated Molecular Interaction DatabaseDetails
Free
iMOTdb - Interacting motifs in proteins databaseDetails
Free
InnateDB - A Knowledge Resource for Innate Immunity Interactions and PathwaysDetails
Free
PSI-MI
INstruct - a database of 3D protein interactome networks with structural resolutionDetails
Free
IntAct - IntAct Molecular Interaction DatabaseDetails
Free
PSI-MI
INTERACT - INTERACT Protein-protein interaction databaseDetailsUnavailable
Interactome - Krogan Lab Interactome DatabaseDetails
Free
InterDom - Database of Interacting DomainsDetailsAcademic
InterEvol - InterEvolDetails
Free
Interfaces - DATASET OF PROTEIN-PROTEIN INTERFACESDetails
Free
InterMitoBase - InterMitoBaseDetails
Free
Interolog - Interolog/Regulog DatabaseDetails
Free
InteroPorc - Automatic molecular interaction predictionsDetails
Free
PSI-MI
InterPare - The Protein Interfaceome DatabaseDetailsUnavailable
InterPreTS - Interaction Prediction through Tertiary StructureDetailsAcademic
IntNetDB - Integrated Protein Interaction Network DatabaseDetailsUnavailable
IntPath - Integrated Pathway Gene Relationship DatabaseDetails
Free
iPfam - Protein families database of alignments and HMMsDetails
Free
iPPI-DB - Inhibitors of Protein-Protein Interaction DatabaseDetails
Free
iProClass - iProClassDetails
Free
iRefIndex - Interaction Reference IndexDetails
Free
PSI-MI
iRefWeb - Interaction Reference Index Web InterfaceDetails
Free
PSI-MI
IRView - IRViewDetails
Free
PSI-MI
JAIL - JAILDetails
Free
JET2 Viewer - Details
Free
KBDOCK - A Resource for Knowledge-Based Protein DockingDetails
Free
KDBI - Kinetic Data of Bio-molecular Interactions databaseDetailsUnavailable
KIDFamMap - Kinase-Inhibitor-Disease Family MapDetails
Free
KinaseDB - Kinase Pathway DatabaseDetails
Free
KUPS - The University of Kansas Proteomics ServiceDetails
Free
LMPID - Linear Motif mediated Protein-Protein Interaction DatabaseDetails
Free
MatrixDB - Extracellular Matrix Interactions DatabaseDetails
Free
PSI-MI
MetaCore - MetaCore pathway databaseDetailsLicense
BioPAX
SBML
MHCPEP - Database of MHC binding peptidesDetailsUnavailable
MiasDB - Details
Free
MiMI - Michigan Molecular InteractionsDetails
Free
PSI-MI
MINT - Molecular Interaction DatabaseDetails
Free
PSI-MI
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
MIPS MPact - Protein Interaction and Complex DatabaseDetailsUnavailable
PSI-MI
MIPS-MPPI - MIPS Mammalian Protein-Protein Interaction DatabaseDetails
Free
PSI-MI
miRIAD - intragenic microRNA databaseDetailsAcademic
MiST2 - Microbial Signal Transduction DatabaseDetails
Free
MitoInteractome - Mitochondrial Protein Interactome DatabaseDetails
Free
PSI-MI
MitoP2 - Mitochondrial Proteome Details
Free
MMDB - Molecular Modeling DatabaseDetails
Free
MnM - Minimotif MinerDetails
Free
MobiDB - a database of protein disorder and mobility annotationsDetails
Free
ModBase - ModBaseDetails
Free
MPI-LIT - The Microbial Protein Interaction DatabaseDetails
Free
MPID - Magnaporthe grisea Protein-protein Interaction DatabaseDetails
Free
MPID-T - MHC-Peptide Interaction DatabaseDetails
Free
MPID-T2 - MHC-Peptide Interaction Database-TRDetails
Free
MPIDB - Microbial Protein Interaction DatabaseDetails
Free
MppDB - Mouse Protein-Protein Interaction DatabaseDetails
Free
MYCbase - A Database of MYCDetailsAcademic
MycoPathPD - Human Fungal Pathogens Proteome DatabaseDetailsLicense
NCG - Network of Cancer GenesDetails
Free
NCPI - Neurospora Crassa Protein Interactome DatabaseDetails
Free
Negatome - The Negatome DatabaseDetails
Free
NetPro - Molecular Connections Database of Protein InteractionsDetailsLicense
NetworKIN - NetworKINDetails
Free
NeXO - The Network Extracted OntologyDetails
Free
NURSA - Nuclear Receptor Signaling AtlasDetails
Free
ooTFD - Object Oriented Transcription Factors DatabaseDetailsAcademic
PAGED - Pathway and Gene Enrichment DatabaseDetails
Free
PAIR - The Predicted Arabidopsis Interactome ResourceDetails
Free
PSI-MI
Pathcalling - Curagen PathcallingDetailsUnavailable
PathCards - Pathway Unification DatabaseDetails
Free
PathDB - Pathways DatabaseDetailsUnavailable
Pathway Studio - Pathway StudioDetailsLicense
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PATRIC - PathoSystems Resource Integration CenterDetails
Free
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PCDB - Protein Conformational DatabaseDetails
Free
PCPPI - Penicillium-Crop Protein-Protein Interactions databaseDetailsAcademic
PCRPi-DB - Presaging Critical Residues in Protein interfaces-DataBaseDetails
Free
PDBeMotif - Protein Data Bank in Europe, Motifs and SitesDetails
Free
PDBsum - PDBsum: pictorial database of 3D structures in the Protein Data BankDetails
Free
PDZBase - PDZ domain protein-protein interaction databaseDetails
Free
PepBank - PepBank Peptide DatabaseDetails
Free
PepCyber - PepCyber: P~PepDetails
Free
PSI-MI
PeroxisomeDB - Peroxisome DatabaseDetails
Free
Phospho.ELM - Post-translational phosphorylation databaseDetails
Free
PhosphoBase - Database of phosphorylation sitesDetails
Free
PhosphoGRID - PhosphoGRIDDetails
Free
PhosphoNetworks - PhosphoNetworksDetailsAcademic
PhosphoPOINT - PhosphoPOINTDetails
Free
PhosphoSite - Cell Signaling Technology's PhosphoSite DatabaseDetailsAcademic
BioPAX
PI2PE - Protein Interface/Interior Prediction EngineDetails
Free
PIBASE - PIBASEDetails
Free
PICCOLO - PICCOLODetails
Free
PIG - Host Pathogen InteractionsDetails
Free
Pigment Cell Gene Resource - Pigment Cell Gene ResourceDetails
Free
PIMADb - Database of Protein-Protein Interactions in Macromolecular AssembliesDetails
Free
PIMRider - Protein Interaction Map - HybrigenicsDetailsLicense
PSI-MI
PINA - Protein Interaction Network AnalysisDetails
Free
PINdb - Proteins Interacting in the Nucleus databaseDetails
Free
PINT - Protein-protein Interactions Thermodynamic DatabaseDetails
Free
PIPs - Human Protein-Protein Interaction PredictionDetails
Free
PiSITE - Database of Protein Interaction SITEsDetails
Free
PlantPAN - Plant Promoter Analysis NavigatorDetailsAcademic
POINT - Prediction of InteractomeDetails
Free
PombePD - Schizosaccharomyces pombe Proteome DatabaseDetailsLicense
PPID - Protein-Protein Interaction DatabaseDetailsLicense
PPIRA - Protein-Protein Interactions between Ralstonia solanacearum and Arabidopsis thalianaDetails
Free
PPIV (FANTOM) - RIKEN FANTOM Protein Protein Interaction ViewerDetailsUnavailable
PQS - Protein Quaternary Structure databaseDetails
Free
Predictome - PredictomeDetails
Free
prePPI - prePPIDetails
Free
PRIME - Protein interaction and molecular information databaseDetailsUnavailable
PRIMOS - Protein Interaction and Molecule Search databaseDetails
Free
PRIN - Predicted Rice Interactome DatabaseDetails
Free
PRISM - Protein Interactions by Structural MatchingDetails
Free
ProChart - ProChart database of signal transduction pathway informationDetailsUnavailable
PROFESS - Protein Function, Evolution, Structure and Sequence DatabaseDetails
Free
Prolinks - ProlinksDetails
Free
ProMesh - ProMesh Protein-Protein Interaction DatabaseDetailsUnavailable
PROMISCUOUS - PROMISCUOUSDetails
Free
ProNet - Protein-protein Interaction DatabaseDetailsUnavailable
ProtCID - PROTein Common Interfaces DatabaseDetails
Free
PROTCOM - Database of Protein ComplexesDetailsUnavailable
Protein Lounge - Protein LoungeDetailsLicense
Proteome - DetailsLicense
PSIbase - Protein Structural Interactome DatabaseDetails
Free
PSICQUIC - Proteomics Standards Initiative Common QUery InterfaCeDetails
Free
PSI-MI
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
PTMcode - PTMcode 2Details
Free
PubAngioGen - Public AngioGenesis research portalDetails
Free
PubGene - PubGeneDetails
Free
PutidaNET - PutidaNETDetails
Free
RAPID - Resource of Asian Primary Immunodeficiency DiseasesDetails
Free
RegPhos - Regulatory Network in Protein PhosphorylationDetails
Free
RGD - Rat Genome Database pathway resourceDetails
Free
RiceGeneThresher - RiceGeneThresher: bioinformatics tool site for rice genes discoveryDetails
Free
RKD - Rice Kinase DatabaseDetails
Free
S/MARt_DB - The S/MAR transaction DataBaseDetailsAcademic
Scansite - ScansiteDetails
Free
SCOPPI - Structural classification of protein-protein interfacesDetails
Free
SCOWLP - structural classification of protein binding reasons for atomic comparative analysis of protein interactionsDetails
Free
SGD Pathway Tools - Saccharomyces Genome Database Pathway ToolsDetails
Free
BioPAX
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule PagesDetails
Free
BioPAX
SBML
SignaLink 2 - SignaLink 2: a multi-layered signaling pathway resourceDetailsAcademic
PSI-MI
BioPAX
SBML
SIGNOR - The SIGnaling Network Open ResourceDetails
Free
SBML
Snap - a Single Nucleotide Polymorphism Annotation PlatformDetails
Free
SNAPPI-DB - Structures, iNterfaces and Alignments for Protein-Protein InteractionsDetails
Free
SPiD - Subtilis Protein interaction DatabaseDetailsUnavailable
SPIDer - Saccharomyces Protein-protein Interaction DatabaseDetails
Free
SPIN-PP - Surface Properties of Interfaces - Protein-Protein InterfacesDetailsUnavailable
SpliceAid-F - A Database of Human Splicing Factors and their Binding SitesDetails
Free
Spliceosome Database - Details
Free
SPPS - Sequence-based Protein Partner SearchDetails
Free
STRING - Search Tool for the Retrieval of Interacting Genes/ProteinsDetailsLicense
Struct2Net - Structure-based Computational Predictions of Protein-Protein InteractionsDetails
Free
SUBA3 - The SUBcellular localization database for Arabidopsis proteinsDetails
Free
SuperTarget - SuperTargetDetails
Free
SYFPEITHI - Database of MHC Ligands and Peptide MotifsDetailsLicense
SYNDB - Synapse DatabaseDetails
Free
SynechoNET - SynechoNet: Integrated Protein-Protein Interaction Database of Synechocystis sp. PCC 6803Details
Free
SynSysNet - Synaptic Proteins DatabaseDetails
Free
T2D-Db - T2D-Db: An Integrated Data Resource on Type 2 DiabetesDetails
Free
TeloPIN - Telomeric Proteins Interaction NetworkDetails
Free
TissueNet - The Database of Human Tissue Protein-Protein InteractionsDetails
Free
TRIP - Mammalian Transient Receptor Potential Channel-Interacting ProteinDetails
Free
Ulysses - Projection of Protein Networks across SpeciesDetailsUnavailable
UniHI - Unified Human InteractomeDetails
Free
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictionsDetails
Free
VHLdb - a database of pVHL interactions and mutationsDetails
Free
VirHostNet - Virus-Host NetworkDetails
Free
PSI-MI
Virus Mentha - The Viral Interactomes BrowserDetails
Free
VirusMINT - VirusMINTDetails
Free
PSI-MI
Wiki-Pi - Wiki-Pi: a wiki resource centred on human protein-protein interactionsDetails
Free
WormBase - Worm BaseDetails
Free
WormPD - Caenorhabditis elegans Proteome DatabaseDetailsLicense
XooNET - Integrated Protein-Protein Interaction database of Xanthomonas oryzae pathovar oryzae KACC1031Details
Free
yApoptosis - yeast apoptosis databaseDetails
Free
SBML
Yeast KID - Yeast Kinase Interaction DatabaseDetails
Free
yeastnet - A Consensus Reconstruction of Yeast MetabolismDetails
Free
SBML
YPA - Yeast Promoter AtlasDetails
Free
YPD - Yeast Proteome DatabaseDetailsLicense
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Metabolic Pathways  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
AcypiCyc - Acyrthosiphon pisum Metabolic PathwaysDetails
Free
BioPAX
AHD2.0 - Arabidopsis Hormone Database 2.0Details
Free
aMAZE - Protein Function and Biochemical Pathways ProjectDetailsUnavailable
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
AraCyc - Arabidopsis enzymes and biochemical pathways database Details
Free
AraPath - AraPath: a knowledgebase for pathway analysis in ArabidopsisDetailsAcademic
ArthropodaCyc - Details
Free
BioPAX
ASD - Allosteric DatabaseDetails
Free
AtIPD - Arabidopsis thaliana Isoprenoid Pathway DatabaseDetails
Free
BESC BeoCyc - BioEnergy Science Center BeoCycDetails
Free
BioPAX
BiGG Models - DetailsAcademic
SBML
BioCyc - BioCyc Knowledge LibraryDetailsLicense
BioPAX
SBML
BiologicalNetworks - BiologicalNetworksDetailsUnavailable
BioModels - BioModels DatabaseDetails
Free
BioPAX
SBML
CellML
Bionemo - Biodegradation Network Molecular Biology DatabaseDetails
Free
Biopath - Biochemical Pathways databaseDetailsLicense
BioSilico - BioSilicoDetails
Free
Biozon - BiozonDetails
Free
BRENDA - BRaunschweig ENzyme DAtabaseDetailsAcademic
SBML
BsubCyc - BsubCycDetailsLicense
BioPAX
SBML
CADgene - Coronary Artery Disease Gene DatabaseDetails
Free
CathaCyc - CathaCyc: Metabolic Pathway Database of Catharanthus roseusDetails
Free
BioPAX
CellML Repository - CellML Model RepositoryDetails
Free
CellML
CPDB - ConsensusPathDBDetailsAcademic
PSI-MI
Cyclonet - CyclonetDetails
Free
dbSNO - database of Cysteine S-NitrOsylationDetails
Free
DEOP - Dragon Explorer of Osmoprotection PathwaysDetailsAcademic
DEPOD - the human DEPhOsphorylation DatabaseDetails
Free
PSI-MI
ECMDB - E. Coli Metabolome DatabaseDetails
Free
EcoCyc - Encyclopedia of E. coli Genes and MetabolismDetailsAcademic
BioPAX
SBML
EMP - Enzymes and Metabolic Pathways DatabaseDetailsUnavailable
ENZYME - Enzyme nomenclature databaseDetails
Free
Enzyme Portal - EBI Enzyme PortalDetails
Free
ERGO - ERGO Genome Analysis and Discovery SystemDetailsLicense
ExPASy Biochemical Pathways - ExPASy - Roche Applied Science Biochemical PathwaysDetails
Free
EXPath - Comparative Expression Analysis Inferring Metabolic Pathways for PlantsDetails
Free
FlyMine - FlyMineDetails
Free
FlyReactome - FlyReactome: a curated knowledgebase of drosophila melanogaster pathwaysDetails
Free
BioPAX
SBML
FMM - From Metabolite to MetaboliteDetails
Free
GDR Cyc Pathways - Genome Database for Rosaceae Cyc PathwaysDetails
Free
BioPAX
GeneGlobe - GeneGlobeDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeneNet - Genetic NetworksDetails
Free
GenMAPP - Gene MicroArray Pathway ProfilerDetailsUnavailable
GLAMM - Genome-Linked Application for Metabolic MapsDetails
Free
GO - Gene Ontology ConsortiumDetails
Free
GOLD.db - Genomics of Lipid-associated DisordersDetails
Free
GRAMENE - Plant Metabolic PathwaysDetails
Free
H-InvDB - H-InvDB: Annotated Human Gene DatabaseDetails
Free
hiPathDB - human integrated Pathway DB with facile visualizationDetails
Free
HMDB - Human Metabolome DatabaseDetails
Free
HPD - Human Pathway DatabaseDetails
Free
HumanCyc - Encyclopedia of Homo sapiens genes and metabolismDetailsLicense
BioPAX
SBML
IMG - Integrated Microbial GenomesDetails
Free
IMID - Integrated Molecular Interaction DatabaseDetails
Free
IMP - Integrative Multi-species PredictionDetails
Free
Indigo - Gene Neighborhoods and Codon UsageDetailsUnavailable
IntEnz - Integrated relational Enzyme databaseDetails
Free
BioPAX
IntPath - Integrated Pathway Gene Relationship DatabaseDetails
Free
IPAD - the Integrated Pathway Analysis Database for Systematic Enrichment AnalysisDetails
Free
iPath - interactive Pathways ExplorerDetails
Free
iPAVS - Integrated Pathway Resources, Analysis and Visualization SystemDetails
Free
BioPAX
SBML
iProClass - iProClassDetails
Free
JWS Online - Online Cellular Systems ModellingDetails
Free
SBML
KaPPA-View - Kazusa Plant Pathway ViewerDetails
Free
KEGG - Kyoto Encyclopedia of Genes and GenomesDetailsAcademic
BioPAX
kPath - Details
Free
BioPAX
LAMP - (Liverpool) Library of Apicomplexan Metabolic PathwaysDetails
Free
LIGAND - Molecular building blocks of life in the chemical spaceDetails
Free
LIPID MAPS - LIPID Metabolites and Pathways StrategyDetails
Free
MaizeCyc - MaizeCyc: metabolic pathways in maizeDetails
Free
BioPAX
MedicCyc 2.0 - Medicago truncatula Pathway DatabaseDetails
Free
BioPAX
MEMOSys - MEtabolic MOdel SystemDetails
Free
SBML
MetaCore - MetaCore pathway databaseDetailsLicense
BioPAX
SBML
MetaCrop - MetaCropDetails
Free
SBML
MetaCyc - Metabolic Pathway DatabaseDetailsAcademic
BioPAX
SBML
metaTIGER - metaTIGER: metabolic gene evolution resourceDetails
Free
MetExplore - Details
Free
SBML
MetNetDB - Metabolic Network ExchangeDetails
Free
SBML
Millipore Pathways - Your online source for visualizing metabolic and signaling pathwaysDetails
Free
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
MitoProteome - Human Mitochondrial Protein DatabaseDetails
Free
MMMDB - Mouse Multiple tissue Metabolome DataBaseDetails
Free
MODOMICS - Modomics: a database of RNA modification pathwaysDetails
Free
Monod - Modeler's Notebook and DatastoreDetails
Free
MouseCyc - Mouse Pathway DatabaseDetails
Free
BioPAX
MouseNetV2 - Probabilistic Functional Gene Network for Laboratory Mouse, Mus musculusDetails
Free
MPB - Metabolic Pathways of BiochemistryDetailsUnavailable
MPMP - Malaria Parasite Metabolic PathwaysDetails
Free
MRAD - Metabolic Reaction Analysis DatabaseDetailsUnavailable
MYCbase - A Database of MYCDetailsAcademic
NCBI BioSystems - NCBI BioSystemsDetails
Free
Nematode.net - Nematode.netDetails
Free
NetBiochem - Medical Biochemistry ResourceDetails
Free
Nicholson Minimaps - IUBMB-Nicholson Metabolic Maps, Minimaps & AnimapsDetails
Free
PAGED - Pathway and Gene Enrichment DatabaseDetails
Free
PathArt - Pathway ArticulatorDetailsLicense
PathCards - Pathway Unification DatabaseDetails
Free
PathCase - CASE Pathways Database SystemDetails
Free
BioPAX
PathDB - Pathways DatabaseDetailsUnavailable
pathDIP - Pathway Data Integration PortalDetails
Free
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PATIKA - Pathway Analysis Tool for Integration and Knowledge AcquisitionDetailsAcademic
PATRIC - PathoSystems Resource Integration CenterDetails
Free
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDS - Pathways Database SystemDetailsUnavailable
PeroxisomeDB - Peroxisome DatabaseDetails
Free
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge BaseDetails
Free
BioPAX
Plant Reactome - Plant Reactome Pathway DatabaseDetails
Free
PSI-MI
BioPAX
SBML
PlantCyc - Plant Metabolic Pathway DatabasesDetails
Free
BioPAX
PlasmoDB - Plasmodium Genomics ResourceDetails
Free
PMAP - The Proteolysis MapDetails
Free
PolymiRTS DB - Polymorphism in microRNAs and their TargetSitesDetails
Free
ProcessDB - ProcessDBDetailsLicense
PROMISCUOUS - PROMISCUOUSDetails
Free
Protein Lounge - Protein LoungeDetailsLicense
Proteome - DetailsLicense
PUMA2 - Evolutionary Analysis of MetabolismDetailsUnavailable
Reactome - Reactome KnowledgeBaseDetails
Free
PSI-MI
BioPAX
SBML
RegPhos - Regulatory Network in Protein PhosphorylationDetails
Free
RGD - Rat Genome Database pathway resourceDetails
Free
RiceCyc - The rice metabolic pathway databaseDetails
Free
RiceGeneThresher - RiceGeneThresher: bioinformatics tool site for rice genes discoveryDetails
Free
RNApathwaysDB - RNA Pathways Database: a database of RNA maturation and decayDetails
Free
SABIO-RK - SABIO-Reaction Kinetics DatabaseDetails
Free
BioPAX
SBML
SBML Model Repository - SBML Model RepositoryDetailsUnavailable
SBML
SGD Pathway Tools - Saccharomyces Genome Database Pathway ToolsDetails
Free
BioPAX
SGN - Sol Genomics NetworkDetails
Free
SMPDB - Small Molecule Pathway DatabaseDetails
Free
BioPAX
SBML
Snap - a Single Nucleotide Polymorphism Annotation PlatformDetails
Free
SomamiR DB - Somatic mutations altering microRNA-ceRNA interactionsDetails
Free
SoyBase - USDA-ARS Soybean Genetics and Genome DatabaseDetails
Free
SoyFN - Soybean Functional NetworkDetails
Free
SubtiPathways - SubtiPathwaysDetails
Free
SuperTarget - SuperTargetDetails
Free
SYNDB - Synapse DatabaseDetails
Free
SynSysNet - Synaptic Proteins DatabaseDetails
Free
SysPTM - A Systematic Resource for Post-Translational ModificationDetails
Free
SYSTOMONAS - SYSTems biology of pseudOMONASDetails
Free
T2D-Db - T2D-Db: An Integrated Data Resource on Type 2 DiabetesDetails
Free
TAIR - The Arabidopsis Information ResourceDetails
Free
TDR Targets Database - The Tropical Disease Research Targets DatabaseDetails
Free
TECR - Thermodynamics of Enzyme-Catalyzed ReactionsDetails
Free
The SEED - Details
Free
TRANSPATH - TRANSPATHDetailsLicense
Trypanocyc - The Pathway/Genome Database of Trypanosoma bruceiDetails
Free
BioPAX
SBML
UM-BBD - Biocatalysis/Biodegradation DatabaseDetails
Free
UniPathway - UniPathway: a resource for the exploration of metabolic pathwaysDetails
Free
WholeCellKB - WholeCellKB: Mycoplasma Genitalium DatabaseDetails
Free
Wiki-Pi - Wiki-Pi: a wiki resource centred on human protein-protein interactionsDetails
Free
WikiPathways - WikiPathwaysDetails
Free
BioPAX
WIT - What Is There?DetailsUnavailable
WITHDRAWN - A Resource for Withdrawn and Discontinuous DrugsDetails
Free
yeastnet - A Consensus Reconstruction of Yeast MetabolismDetails
Free
SBML
YMDB - The Yeast Metabolome DatabaseDetails
Free
Back to the Top

Signaling Pathways  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
AgingChart - Aging ChartDetails
Free
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
AraPath - AraPath: a knowledgebase for pathway analysis in ArabidopsisDetailsAcademic
ASD - Allosteric DatabaseDetails
Free
BiologicalNetworks - BiologicalNetworksDetailsUnavailable
BioModels - BioModels DatabaseDetails
Free
BioPAX
SBML
CellML
CA1Neuron - Pathways of the hippocampal CA1 neuronDetailsUnavailable
Cancer Cell Map - The Cancer Cell MapDetails
Free
BioPAX
CBN - Causal Biological Networks DatabaseDetails
Free
CCDB - The Cell Cycle DatabaseDetails
Free
SBML
CellML Repository - CellML Model RepositoryDetails
Free
CellML
CHD@ZJU - Coronary Heart Disease @ZJU DatabaseDetails
Free
COPE - Cytokines and Cells Online Pathfinder EncyclopediaDetailsLicense
CPDB - ConsensusPathDBDetailsAcademic
PSI-MI
CSNDB - Cell Signaling Networks DatabaseDetailsUnavailable
CST - Cell Signaling Technology Pathway DatabaseDetails
Free
Cyclonet - CyclonetDetails
Free
dbSNO - database of Cysteine S-NitrOsylationDetails
Free
DDRprot - DNA Damage Response proteins databaseDetails
Free
DEPOD - the human DEPhOsphorylation DatabaseDetails
Free
PSI-MI
DNAtraffic - DNAtraffic DatabaseDetails
Free
DOQCS - Database of Quantitative Cellular SignalingDetails
Free
SBML
DSM - Dynamic Signaling MapsDetailsUnavailable
ECMDB - E. Coli Metabolome DatabaseDetails
Free
eMIM - Electronic Molecular Interaction MapDetails
Free
EndoNet - EndoNetDetails
Free
Enzyme Portal - EBI Enzyme PortalDetails
Free
FlyMine - FlyMineDetails
Free
FlyReactome - FlyReactome: a curated knowledgebase of drosophila melanogaster pathwaysDetails
Free
BioPAX
SBML
GDR Cyc Pathways - Genome Database for Rosaceae Cyc PathwaysDetails
Free
BioPAX
GeneGlobe - GeneGlobeDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeneNet - Genetic NetworksDetails
Free
GeneTex - GeneTexDetails
Free
GenMAPP - Gene MicroArray Pathway ProfilerDetailsUnavailable
GO - Gene Ontology ConsortiumDetails
Free
GOLD.db - Genomics of Lipid-associated DisordersDetails
Free
GON - Genomic Object NetDetails
Free
HCPIN - Human Cancer Protein Interaction NetworkDetails
Free
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsUnavailable
hiPathDB - human integrated Pathway DB with facile visualizationDetails
Free
HPD - Human Pathway DatabaseDetails
Free
HumanCyc - Encyclopedia of Homo sapiens genes and metabolismDetailsLicense
BioPAX
SBML
IMID - Integrated Molecular Interaction DatabaseDetails
Free
InnateDB - A Knowledge Resource for Innate Immunity Interactions and PathwaysDetails
Free
PSI-MI
INOH - Integrating Network Objects with HierarchiesDetails
Free
BioPAX
iPath - interactive Pathways ExplorerDetails
Free
iPAVS - Integrated Pathway Resources, Analysis and Visualization SystemDetails
Free
BioPAX
SBML
iProClass - iProClassDetails
Free
JWS Online - Online Cellular Systems ModellingDetails
Free
SBML
LIPID MAPS - LIPID Metabolites and Pathways StrategyDetails
Free
MACPAK - Simulatable Macrophage Pathway KnowledgebaseDetails
Free
MetaCore - MetaCore pathway databaseDetailsLicense
BioPAX
SBML
Millipore Pathways - Your online source for visualizing metabolic and signaling pathwaysDetails
Free
miRror-Suite - A Dual View on Sets of microRNAs and their TargetsDetails
Free
MiST2 - Microbial Signal Transduction DatabaseDetails
Free
MitoProteome - Human Mitochondrial Protein DatabaseDetails
Free
Monod - Modeler's Notebook and DatastoreDetails
Free
MouseNetV2 - Probabilistic Functional Gene Network for Laboratory Mouse, Mus musculusDetails
Free
NCBI BioSystems - NCBI BioSystemsDetails
Free
Nematode.net - Nematode.netDetails
Free
NetPath - NetPath: Signal Transduction PathwaysDetails
Free
PSI-MI
BioPAX
SBML
NetSlim - NetSlimDetails
Free
PSI-MI
BioPAX
SBML
OmniPath - OmniPathDetails
Free
Ontocancro - OntocancroDetails
Free
BioPAX
PAGED - Pathway and Gene Enrichment DatabaseDetails
Free
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsDetails
Free
BioPAX
SBML
PathArt - Pathway ArticulatorDetailsLicense
PathCards - Pathway Unification DatabaseDetails
Free
PathDB - Pathways DatabaseDetailsUnavailable
pathDIP - Pathway Data Integration PortalDetails
Free
PathoPlant - PathoPlantDetails
Free
Pathway Studio - Pathway StudioDetailsLicense
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PATIKA - Pathway Analysis Tool for Integration and Knowledge AcquisitionDetailsAcademic
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDS - Pathways Database SystemDetailsUnavailable
PhosphoSite - Cell Signaling Technology's PhosphoSite DatabaseDetailsAcademic
BioPAX
PID - NCI-Nature Pathway Interaction DatabaseDetailsUnavailable
BioPAX
Plant Reactome - Plant Reactome Pathway DatabaseDetails
Free
PSI-MI
BioPAX
SBML
PMAP - The Proteolysis MapDetails
Free
PolymiRTS DB - Polymorphism in microRNAs and their TargetSitesDetails
Free
ProcessDB - ProcessDBDetailsLicense
PROMISCUOUS - PROMISCUOUSDetails
Free
Protein Lounge - Protein LoungeDetailsLicense
Proteome - DetailsLicense
PRRDB - Pattern Recognition Receptor DatabaseDetails
Free
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
PubAngioGen - Public AngioGenesis research portalDetails
Free
Reactome - Reactome KnowledgeBaseDetails
Free
PSI-MI
BioPAX
SBML
RegPhos - Regulatory Network in Protein PhosphorylationDetails
Free
REPAIRtoire - REPAIRtoire: a database of DNA repair pathwaysDetails
Free
RGD - Rat Genome Database pathway resourceDetails
Free
ROSPath - Reactive Oxygen Species related Signaling PathwayDetails
Free
SBML Model Repository - SBML Model RepositoryDetailsUnavailable
SBML
Sentra - Sentra Signal Transduction DatabaseDetailsUnavailable
SIGMA-ALDRICH - Cell Signalling Pathway Slides & ChartsDetailsUnavailable
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule PagesDetails
Free
BioPAX
SBML
SignaLink 2 - SignaLink 2: a multi-layered signaling pathway resourceDetailsAcademic
PSI-MI
BioPAX
SBML
SIGNOR - The SIGnaling Network Open ResourceDetails
Free
SBML
SigPath - Signaling Pathway Information SystemDetails
Free
SMPDB - Small Molecule Pathway DatabaseDetails
Free
BioPAX
SBML
SomamiR DB - Somatic mutations altering microRNA-ceRNA interactionsDetails
Free
SoyFN - Soybean Functional NetworkDetails
Free
SPAD - Signaling Pathway DatabaseDetails
Free
SPIKE - Signaling Pathway Integrated Knowledge EngineDetailsAcademic
BioPAX
STCDB - Signal Transduction Classification DatabaseDetails
Free
STKE - Signal Transduction Knowledge EnvironmentDetailsAcademic
SBML
SuperTarget - SuperTargetDetails
Free
SynSysNet - Synaptic Proteins DatabaseDetails
Free
SysPTM - A Systematic Resource for Post-Translational ModificationDetails
Free
T2D-Db - T2D-Db: An Integrated Data Resource on Type 2 DiabetesDetails
Free
TRANSPATH - TRANSPATHDetailsLicense
TRMP - Therapeutically Relevant Multiple Pathways DatabaseDetails
Free
TRRD - Transcription Regulatory Regions DatabaseDetails
Free
Wiki-Pi - Wiki-Pi: a wiki resource centred on human protein-protein interactionsDetails
Free
WikiPathways - WikiPathwaysDetails
Free
BioPAX
WITHDRAWN - A Resource for Withdrawn and Discontinuous DrugsDetails
Free
XPD - Phosphorylation Site DatabaseDetailsUnavailable
XTalkDB - Details
Free
Back to the Top

Pathway Diagrams  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
AcypiCyc - Acyrthosiphon pisum Metabolic PathwaysDetails
Free
BioPAX
AgingChart - Aging ChartDetails
Free
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
ArthropodaCyc - Details
Free
BioPAX
AtIPD - Arabidopsis thaliana Isoprenoid Pathway DatabaseDetails
Free
BBID - Biological Biochemical Image DatabaseDetails
Free
BioCarta - BioCarta Pathway DiagramsDetails
Free
BMPH - Boehringer Mannheim Biochemical Pathways Wall ChartDetails
Free
BsubCyc - BsubCycDetailsLicense
BioPAX
SBML
CBN - Causal Biological Networks DatabaseDetails
Free
CHD@ZJU - Coronary Heart Disease @ZJU DatabaseDetails
Free
CST - Cell Signaling Technology Pathway DatabaseDetails
Free
Cyclonet - CyclonetDetails
Free
DDRprot - DNA Damage Response proteins databaseDetails
Free
Drastic - Database Resource for Analysis of Signal Transduction In CellsDetails
Free
DSM - Dynamic Signaling MapsDetailsUnavailable
ECMDB - E. Coli Metabolome DatabaseDetails
Free
eMIM - Electronic Molecular Interaction MapDetails
Free
EXPath - Comparative Expression Analysis Inferring Metabolic Pathways for PlantsDetails
Free
GDR Cyc Pathways - Genome Database for Rosaceae Cyc PathwaysDetails
Free
BioPAX
GeneGlobe - GeneGlobeDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeneTex - GeneTexDetails
Free
GLAMM - Genome-Linked Application for Metabolic MapsDetails
Free
GRAMENE - Plant Metabolic PathwaysDetails
Free
GTDB - Glycosylation Pathways DatabaseDetails
Free
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsUnavailable
HPRD - Human Protein Reference Database DetailsAcademic
PSI-MI
HumanCyc - Encyclopedia of Homo sapiens genes and metabolismDetailsLicense
BioPAX
SBML
INOH - Integrating Network Objects with HierarchiesDetails
Free
BioPAX
InsectBase - Integrated Genome and Transcriptome Resources for InsectsDetails
Free
IntPath - Integrated Pathway Gene Relationship DatabaseDetails
Free
iPath - interactive Pathways ExplorerDetails
Free
KaPPA-View - Kazusa Plant Pathway ViewerDetails
Free
KEGG - Kyoto Encyclopedia of Genes and GenomesDetailsAcademic
BioPAX
KMIM - Kohn Molecular Interaction MapsDetails
Free
kPath - Details
Free
BioPAX
LAMP - (Liverpool) Library of Apicomplexan Metabolic PathwaysDetails
Free
LIPID MAPS - LIPID Metabolites and Pathways StrategyDetails
Free
MaizeCyc - MaizeCyc: metabolic pathways in maizeDetails
Free
BioPAX
MedicCyc 2.0 - Medicago truncatula Pathway DatabaseDetails
Free
BioPAX
metaTIGER - metaTIGER: metabolic gene evolution resourceDetails
Free
MiMI - Michigan Molecular InteractionsDetails
Free
PSI-MI
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
MPB - Metabolic Pathways of BiochemistryDetailsUnavailable
MPMP - Malaria Parasite Metabolic PathwaysDetails
Free
NCBI BioSystems - NCBI BioSystemsDetails
Free
Nematode.net - Nematode.netDetails
Free
NetBiochem - Medical Biochemistry ResourceDetails
Free
NetSlim - NetSlimDetails
Free
PSI-MI
BioPAX
SBML
Nicholson Minimaps - IUBMB-Nicholson Metabolic Maps, Minimaps & AnimapsDetails
Free
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsDetails
Free
BioPAX
SBML
PathCards - Pathway Unification DatabaseDetails
Free
PathFinder - Cell Signaling PathwaysDetailsUnavailable
Pathway Slides - Cell Signaling Pathway Slides & ChartsDetailsUnavailable
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge BaseDetails
Free
BioPAX
PID - NCI-Nature Pathway Interaction DatabaseDetailsUnavailable
BioPAX
Plant Reactome - Plant Reactome Pathway DatabaseDetails
Free
PSI-MI
BioPAX
SBML
PlasmoDB - Plasmodium Genomics ResourceDetails
Free
PolymiRTS DB - Polymorphism in microRNAs and their TargetSitesDetails
Free
Protein Lounge - Protein LoungeDetailsLicense
PubAngioGen - Public AngioGenesis research portalDetails
Free
Reactome - Reactome KnowledgeBaseDetails
Free
PSI-MI
BioPAX
SBML
RGD - Rat Genome Database pathway resourceDetails
Free
SGN - Sol Genomics NetworkDetails
Free
SIGMA-ALDRICH - Cell Signalling Pathway Slides & ChartsDetailsUnavailable
SignaLink 2 - SignaLink 2: a multi-layered signaling pathway resourceDetailsAcademic
PSI-MI
BioPAX
SBML
SomamiR DB - Somatic mutations altering microRNA-ceRNA interactionsDetails
Free
SPAD - Signaling Pathway DatabaseDetails
Free
SPIKE - Signaling Pathway Integrated Knowledge EngineDetailsAcademic
BioPAX
SynSysNet - Synaptic Proteins DatabaseDetails
Free
T1DBase - Type 1 Diabetes DatabaseDetailsUnavailable
TRMP - Therapeutically Relevant Multiple Pathways DatabaseDetails
Free
Trypanocyc - The Pathway/Genome Database of Trypanosoma bruceiDetails
Free
BioPAX
SBML
VirHostNet - Virus-Host NetworkDetails
Free
PSI-MI
WikiPathways - WikiPathwaysDetails
Free
BioPAX
WITHDRAWN - A Resource for Withdrawn and Discontinuous DrugsDetails
Free
Back to the Top

Transcription Factors / Gene Regulatory Networks  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
ABS - Annotated regulatory Binding SitesDetails
Free
AGRIS - Arabidopsis Gene Regulatory Information ServerDetails
Free
aMAZE - Protein Function and Biochemical Pathways ProjectDetailsUnavailable
AnimalTFDB - Animal Transcription Factor DatabaseDetails
Free
Argonaute - Gene regulation by mammalian micro-RNAsDetailsUnavailable
AthaMap - AthaMapDetails
Free
Athena - AthenaDetails
Free
AtPAN - Arabidopsis thaliana Promoter Analysis NetDetails
Free
AURA - Atlas of UTR Regulatory ActivityDetails
Free
BioPathway Visualizer - Arizona BioPathway VisualizerDetailsUnavailable
BSRD - Bacterial Small Regulatory RNA DatabaseDetails
Free
ChIPBase - Details
Free
CircNet - A Database of Circular RNAsDetails
Free
cisRED - Cis-regulatory element databaseDetails
Free
CollecTF - A Database of Transcription Factor Binding Sites in the Bacteria DomainDetails
Free
COMPEL - Database on Composite Regulatory ElementsDetailsUnavailable
CoopTFD - Cooperative Transcription Factors DatabaseDetails
Free
CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory NetworksDetails
Free
CPDB - ConsensusPathDBDetailsAcademic
PSI-MI
DATF - Database of Arabidopsis Transcription FactorsDetails
Free
DBD - DNA-Binding Domain: Transcription Factor Predictor DatabaseDetails
Free
DBTBS - Database of Bacillus subtilis Promoters and Transcription FactorsDetails
Free
DBTGR - DataBase of Tunicate Gene RegulationDetails
Free
Digital Development Database - Lineage Differentiation and Phenotypes in C. elegansDetails
Free
DPInteract - DNA-Protein Interactions DatabaseDetails
Free
DPRP - A Database of Phenotype-Specific Regulatory Programs Derived From Transcription Factor Binding DataDetails
Free
DRTF - Database of Rice Transcription FactorsDetails
Free
ECRbase - Evolutionary conserved region databaseDetails
Free
Expresso - Exploring the Interaction of Transcription Factors and Their Target Genes in Plants using ChIP-Seq DataDetails
Free
FlyFactorSurvey - FlyFactorSurvey: Database of Drosophila TF DNA-Binding SpecifitiesDetails
Free
FlyTF - The Drosophila Transcription Factor DatabaseDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeNet - Gene Networks DatabaseDetailsUnavailable
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsUnavailable
HemoPDB - Hematopoiesis Promoter DatabaseDetailsUnavailable
HoxPro - HOX ProDetails
Free
hPDI - Human Protein-DNA InteractomeDetails
Free
HRTBLDb - Hormone Receptor Target Binding Loci DatabaseDetails
Free
HTPSELEX - HTPSELEXDetails
Free
HTRIdb - Human Transcriptional Regulation Interaction DatabaseDetails
Free
Interolog - Interolog/Regulog DatabaseDetails
Free
ITFP - Intergrated Transcription Factor PlatformDetails
Free
JASPAR - JASPAR Transcription Factor Binding Profile DatabaseDetails
Free
LncReg - database for LncRNA regulatory networksDetails
Free
LSPD - The Liver Specific Gene Promoter DatabaseDetails
Free
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of RegulationDetailsAcademic
MetaCore - MetaCore pathway databaseDetailsLicense
BioPAX
SBML
microrna.org - Microrna.org target databaseDetails
Free
miRBase - microRNA DatabaseDetails
Free
miRecords - miRecordsDetails
Free
miRNAMap - MicroRNA MapDetails
Free
MotifMap - MotifMapDetails
Free
MPromDb - Mammalian Promoter DatabaseDetailsUnavailable
MycoRegNet - Mycobacterial transcription factors and regulatory networksDetailsUnavailable
myGRN - my Genetic Regulatory NetworkDetailsAcademic
OnTheFly - A Database of Drosophila melanogaster Transcription Factors and their Binding SitesDetails
Free
ooTFD - Object Oriented Transcription Factors DatabaseDetailsAcademic
ORTI - Open-access Repository of Transcriptional InteractionDetails
Free
P2TF - Predicted Prokaryotic Transcription FactorsDetails
Free
PAGED - Pathway and Gene Enrichment DatabaseDetails
Free
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PAZAR - A Public Database of Transcription Factor and Regulatory Sequence AnnotationDetails
Free
phiSITE - phiSITE: Database of Gene Regulation in BacteriophagesDetails
Free
PlantCARE - Plant Cis-Acing Regulatory ElementsDetailsAcademic
PlantPAN - Plant Promoter Analysis NavigatorDetailsAcademic
PlantTFDB - Plant Transcription Factor DatabaseDetails
Free
PlnTFDB - Plant Transcription Factor DatabaseDetails
Free
PRODORIC - Prokaryotic database of gene regulationDetailsAcademic
Protein Lounge - Protein LoungeDetailsLicense
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
PTM-Switchboard - Post-Translational Modification-SwitchboardDetails
Free
REDfly - Regulatory Element Database for DrosophilaDetails
Free
RegNetwork - Regulatory Network RepositoryDetails
Free
BioPAX
RegPrecise - RegPrecise: Collection of Manually Curated Inferences of Regulons in Prokaryotic GenomesDetails
Free
RegTransBase - RegTransBaseDetails
Free
RegulonDB - Database on Transcriptional Regulation and Genome OrganizationDetailsAcademic
BioPAX
RiceSRTFDB - The Rice Stress-Responsive Transcription Factor DatabaseDetails
Free
rSNP Guide - rSNP GuideDetails
Free
ScerTF - ScerTFDetails
Free
SCPD - The Promoter Database of Saccharomyces cerevisiaeDetailsAcademic
Sporeweb - Details
Free
STIFDB - Stress Responsive Transcription Factor DatabaseDetails
Free
SYSTOMONAS - SYSTems biology of pseudOMONASDetails
Free
TarBase - TarBaseDetails
Free
TcoF-DB - Database of Transcription co-factors and transcription factor interactionsDetails
Free
TetraFGD - Tetrahymena Functional Genomics DatabaseDetails
Free
TFClass - Classification of Human Transcription Factors and Mouse OrthologsDetails
Free
TFe - Transcription Factor encyclopediaDetails
Free
TFinDit - Transcription Factor-DNA Interaction Data DepositoryDetails
Free
The Network Portal - Details
Free
TRACTOR_DB - TRACTOR_DBDetails
Free
TRANSFAC - Transcription Factor DatabaseDetailsLicense
TRED - Transcriptional Regulatory Element DatabaseDetails
Free
TRRD - Transcription Regulatory Regions DatabaseDetails
Free
TRRUST - Transcriptional Regulatory Relationships Unraveled by Sentence-based Text miningDetailsAcademic
TrSDB - A Proteome Database of Transcription FactorsDetails
Free
WormBase - Worm BaseDetails
Free
yApoptosis - yeast apoptosis databaseDetails
Free
SBML
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiaeDetails
Free
YEASTRACT - YEAst Search for Transcriptional Regulators And Consensus TrackingDetails
Free
YPA - Yeast Promoter AtlasDetails
Free
YTRP - Yeast Transcriptional Regulatory Pathway DatabaseDetails
Free
YY1TargetDB - Yin Yang 1 Target DatabaseDetails
Free