Pathway and binary interaction data (interactions, participants) are normalized next and merged into the database. Original reference molecules are replaced with the corresponding BioPAX warehouse objects. Determine which biological pathways are statistically over-represented in a given gene/protein list. new features including interactive network visualisation (without the need to download a Java webstart), Multi-pathway proteins: proteins can belong to more than one pathway Proteins are classified by pathway position (core/non-core) and section (ligand, receptor, mediator, etc.) through the Grand Challenges in Global Health initiative and by Teagasc. Pathway Identifiers Each pathway map is identified by the combination of 2-4 … us an email if you have any other questions. A component is usually a single protein in a given organism, but multiple proteins can sometimes play the same role. All other data is licensed under the terms of the originating database. ... metabolic disease pathways, metabolite signaling pathways and drug-action pathways. Statistics for manually-curated innate immunity relevant molecular interactions. Reactome is a free, open-source, curated and peer-reviewed pathway database. New manually curated interactions are submitted weekly. Contact: innatedb-mail@sfu.ca, A mirror of InnateDB.com hosted by the David Lynn Group in Australia is available at, Download Imported Experimentally Validated Interactions, Access to Interaction Data via Web Services, Gene Ontology Over-representation Analysis. and the Lynn EMBL Australia Group (South Australian Health & Medical Research Institute and Flinders University, Adelaide, Australia). InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of … KEGG PATHWAY is the reference database for pathway mapping in KEGG Mapper. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

InnateDB curated interactions are licensed under the Design Science License. Reactome is a free, open-source, curated and peer-reviewed pathway database. PCC 6803, T2D-Db - T2D-Db: An Integrated Data Resource on Type 2 Diabetes, TeloPIN - Telomeric Proteins Interaction Network, TissueNet - The Database of Human Tissue Protein-Protein Interactions, TRIP - Mammalian Transient Receptor Potential Channel-Interacting Protein, UbiNet - a web resource for exploring Ubiquitination Networks, Ulysses - Projection of Protein Networks across Species, ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions, VHLdb - a database of pVHL interactions and mutations, Virus Mentha - The Viral Interactomes Browser, Wiki-Pi - Wiki-Pi: a wiki resource centred on human protein-protein interactions, WormPD - Caenorhabditis elegans Proteome Database, XooNET - Integrated Protein-Protein Interaction database of Xanthomonas oryzae pathovar oryzae KACC1031, Yeast KID - Yeast Kinase Interaction Database, yeastnet - A Consensus Reconstruction of Yeast Metabolism, AcypiCyc - Acyrthosiphon pisum Metabolic Pathways, Arabidopsis Reactome - A curated knowledgebase of plant biological pathways, AraCyc - Arabidopsis enzymes and biochemical pathways database, AraPath - AraPath: a knowledgebase for pathway analysis in Arabidopsis, AtIPD - Arabidopsis thaliana Isoprenoid Pathway Database, BESC BeoCyc - BioEnergy Science Center BeoCyc, Bionemo - Biodegradation Network Molecular Biology Database, CathaCyc - CathaCyc: Metabolic Pathway Database of Catharanthus roseus, CellML Repository - CellML Model Repository, DEOP - Dragon Explorer of Osmoprotection Pathways, EcoCyc - Encyclopedia of E. coli Genes and Metabolism, EMP - Enzymes and Metabolic Pathways Database, ERGO - ERGO Genome Analysis and Discovery System, ExPASy Biochemical Pathways - ExPASy - Roche Applied Science Biochemical Pathways, EXPath - Comparative Expression Analysis Inferring Metabolic Pathways for Plants, FlyReactome - FlyReactome: a curated knowledgebase of drosophila melanogaster pathways, GDR Cyc Pathways - Genome Database for Rosaceae Cyc Pathways, GenMAPP - Gene MicroArray Pathway Profiler, GLAMM - Genome-Linked Application for Metabolic Maps, GOLD.db - Genomics of Lipid-associated Disorders, hiPathDB - human integrated Pathway DB with facile visualization, HumanCyc - Encyclopedia of Homo sapiens genes and metabolism, IMP - Integrative Multi-species Prediction, Indigo - Gene Neighborhoods and Codon Usage, IntEnz - Integrated relational Enzyme database, IPAD - the Integrated Pathway Analysis Database for Systematic Enrichment Analysis, iPAVS - Integrated Pathway Resources, Analysis and Visualization System, JWS Online - Online Cellular Systems Modelling, KEGG - Kyoto Encyclopedia of Genes and Genomes, LAMP - (Liverpool) Library of Apicomplexan Metabolic Pathways, LIGAND - Molecular building blocks of life in the chemical space, LIPID MAPS - LIPID Metabolites and Pathways Strategy, Macrophages.com - The Macrophage Community Website, MaizeCyc - MaizeCyc: metabolic pathways in maize, MedicCyc 2.0 - Medicago truncatula Pathway Database, MetaNetX - Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks, metaTIGER - metaTIGER: metabolic gene evolution resource, Millipore Pathways - Your online source for visualizing metabolic and signaling pathways, MitoProteome - Human Mitochondrial Protein Database, MMMDB - Mouse Multiple tissue Metabolome DataBase, MODOMICS - Modomics: a database of RNA modification pathways, MouseNetV2 - Probabilistic Functional Gene Network for Laboratory Mouse, Mus musculus, MPMP - Malaria Parasite Metabolic Pathways, MRAD - Metabolic Reaction Analysis Database, mVOC - Microbial Volatile Organic Compound Database, NDEx Public Server - The Network Data Exchange Public Server, NetBiochem - Medical Biochemistry Resource, Nicholson Minimaps - IUBMB-Nicholson Metabolic Maps, Minimaps & Animaps, pathDIP - Pathway Data Integration Portal, PATIKA - Pathway Analysis Tool for Integration and Knowledge Acquisition, PCOSKB - PolyCystic Ovary Syndrome KnowledgeBase, PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge Base, Plant Reactome - Plant Reactome Pathway Database, PlantCyc - Plant Metabolic Pathway Databases, PolymiRTS DB - Polymorphism in microRNAs and their TargetSites, PseudoCyc - A Database of Metabolic Pathways in Pseudomonas aeruginosa PAO1, PUMA2 - Evolutionary Analysis of Metabolism, RiceCyc - The rice metabolic pathway database, RNApathwaysDB - RNA Pathways Database: a database of RNA maturation and decay, SABIO-RK - SABIO-Reaction Kinetics Database, SBML Model Repository - SBML Model Repository, SomamiR DB - Somatic mutations altering microRNA-ceRNA interactions, SoyBase - USDA-ARS Soybean Genetics and Genome Database, SysPTM - A Systematic Resource for Post-Translational Modification, SYSTOMONAS - SYSTems biology of pseudOMONAS, TAIR - The Arabidopsis Information Resource, TDR Targets Database - The Tropical Disease Research Targets Database, TECR - Thermodynamics of Enzyme-Catalyzed Reactions, Trypanocyc - The Pathway/Genome Database of Trypanosoma brucei, UM-BBD - Biocatalysis/Biodegradation Database, UniPathway - UniPathway: a resource for the exploration of metabolic pathways, WholeCellKB - WholeCellKB: Mycoplasma Genitalium Database, WITHDRAWN - A Resource for Withdrawn and Discontinuous Drugs, AlzPathway - A Comprehensive Map of Signaling Pathways of Alzheimer's Disease, CBN - Causal Biological Networks Database, COPE - Cytokines and Cells Online Pathfinder Encyclopedia, CST - Cell Signaling Technology Pathway Database, DC Pathway - Dendritic Cell Signaling Pathway Map, DDRprot - DNA Damage Response proteins database, DOQCS - Database of Quantitative Cellular Signaling, eMIM - Electronic Molecular Interaction Map, Hedgehog - Hedgehog Signaling Pathway Database, INOH - Integrating Network Objects with Hierarchies, MACPAK - Simulatable Macrophage Pathway Knowledgebase, miRror-Suite - A Dual View on Sets of microRNAs and their Targets, NetPath - NetPath: Signal Transduction Pathways, PANTHER - Protein ANalysis THrough Evolutionary Relationships, PID - NCI-Nature Pathway Interaction Database, PRRDB - Pattern Recognition Receptor Database, REPAIRtoire - REPAIRtoire: a database of DNA repair pathways, ROSPath - Reactive Oxygen Species related Signaling Pathway, Sentra - Sentra Signal Transduction Database, SIGMA-ALDRICH - Cell Signalling Pathway Slides & Charts, SigPath - Signaling Pathway Information System, SPIKE - Signaling Pathway Integrated Knowledge Engine, STCDB - Signal Transduction Classification Database, STKE - Signal Transduction Knowledge Environment, TRMP - Therapeutically Relevant Multiple Pathways Database, TRRD - Transcription Regulatory Regions Database, BBID - Biological Biochemical Image Database, BMPH - Boehringer Mannheim Biochemical Pathways Wall Chart, Drastic - Database Resource for Analysis of Signal Transduction In Cells, InsectBase - Integrated Genome and Transcriptome Resources for Insects, Pathway Slides - Cell Signaling Pathway Slides & Charts, Abasy Atlas - Across-bacteria systems Atlas, AGRIS - Arabidopsis Gene Regulatory Information Server, Argonaute - Gene regulation by mammalian micro-RNAs, AtPAN - Arabidopsis thaliana Promoter Analysis Net, ATRM - Arabidopsis Transcriptional Regulatory Map, BioPathway Visualizer - Arizona BioPathway Visualizer, BSRD - Bacterial Small Regulatory RNA Database, CirGRDB - Circadian gene and regulators database, CollecTF - A Database of Transcription Factor Binding Sites in the Bacteria Domain, COMPEL - Database on Composite Regulatory Elements, CoopTFD - Cooperative Transcription Factors Database, CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory Networks, DATF - Database of Arabidopsis Transcription Factors, DBD - DNA-Binding Domain: Transcription Factor Predictor Database, DBTBS - Database of Bacillus subtilis Promoters and Transcription Factors, DBTGR - DataBase of Tunicate Gene Regulation, Digital Development Database - Lineage Differentiation and Phenotypes in C. elegans, DPInteract - DNA-Protein Interactions Database, DPRP - A Database of Phenotype-Specific Regulatory Programs Derived From Transcription Factor Binding Data, DRTF - Database of Rice Transcription Factors, ECRbase - Evolutionary conserved region database, Expresso - Exploring the Interaction of Transcription Factors and Their Target Genes in Plants using ChIP-Seq Data, FlyFactorSurvey - FlyFactorSurvey: Database of Drosophila TF DNA-Binding Specifities, FlyTF - The Drosophila Transcription Factor Database, HemoPDB - Hematopoiesis Promoter Database, HRTBLDb - Hormone Receptor Target Binding Loci Database, ITFP - Intergrated Transcription Factor Platform, JASPAR - JASPAR Transcription Factor Binding Profile Database, LncReg - database for LncRNA regulatory networks, LSPD - The Liver Specific Gene Promoter Database, MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, microrna.org - Microrna.org target database, MycoRegNet - Mycobacterial transcription factors and regulatory networks, OnTheFly - A Database of Drosophila melanogaster Transcription Factors and their Binding Sites, ORTI - Open-access Repository of Transcriptional Interaction, P2TF - Predicted Prokaryotic Transcription Factors, PAZAR - A Public Database of Transcription Factor and Regulatory Sequence Annotation, phiSITE - phiSITE: Database of Gene Regulation in Bacteriophages, PlantCARE - Plant Cis-Acing Regulatory Elements, PlantTFDB - Plant Transcription Factor Database, PlnTFDB - Plant Transcription Factor Database, PRODORIC - Prokaryotic database of gene regulation, PRODORIC2 - DNA binding sites for prokaryotic transcription factors, PTM-Switchboard - Post-Translational Modification-Switchboard, REDfly - Regulatory Element Database for Drosophila, RegNetwork - Regulatory Network Repository, RegPrecise - RegPrecise: Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes, RegulonDB - Database on Transcriptional Regulation and Genome Organization, RiceSRTFDB - The Rice Stress-Responsive Transcription Factor Database, SCPD - The Promoter Database of Saccharomyces cerevisiae, STIFDB - Stress Responsive Transcription Factor Database, TcoF-DB - Database of Transcription co-factors and transcription factor interactions, TetraFGD - Tetrahymena Functional Genomics Database, TFClass - Classification of Human Transcription Factors and Mouse Orthologs, TFinDit - Transcription Factor-DNA Interaction Data Depository, TRED - Transcriptional Regulatory Element Database, TRRUST - Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining, TrSDB - A Proteome Database of Transcription Factors, YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae, YEASTRACT - YEAst Search for Transcriptional Regulators And Consensus Tracking, YTRP - Yeast Transcriptional Regulatory Pathway Database, AffinDB - Affinity database for protein-ligand complexes, Binding MOAD - Binding Mother of all Databases, BIPA - Biological Interaction database for Protein-nucleic Acid, CREDO - CREDO: A Structural Interactomics Database For Drug Discovery, CTD - Comparative Toxicogenomics Database, DB-PABP - Database of Polyanion Binding Proteins, Guide to Pharmacology - Guide to Pharmacology, HoPaCI-db - Host-Pseudomonas and Coxiella Interaction DataBase, IUPHAR-DB - The International Union of Basic and Clinical Pharmacology Database, KLIFS - Kinase-Ligand Interaction Fingerprints and Structures database, MATADOR - Manually Annotated Targets and Drugs Online Resource, Metrabase - Metabolism and Transport Database, PDSP Ki Database - Psychoactive Drug Screening Program Ki Database, PLATINUM - Protein-Ligand Affinity Change Upon Mutation Database, PLIC - Protein-Ligand Interaction Clusters, PoSSuM - Pocket Similarity Search using Multi-Sketches, ProtChemSI - ProtChemSI: the database of protein-chemical structural interactions, PSMDB - Protein / Small-molecule database, RCSB PDB - The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Relibase - Protein-ligand database query tool, sc-PDB - An Annotated Database of Druggable Binding Sites from the Protein DataBank, SPLINTER - Structural Protein-Ligand Interactome, STITCH - Chemical-Protein Interaction Networks, SuperCYP - SuperCYP, Cytochrome P450 Database, SwissLipids - A Knowledge Resource for Lipids and their Biology, Transformer - Metabolism of Xenobiotics Database, UniPROBE - Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation, AraNet - AraNet: Probabilistic Functional Gene Network of Arabidopsis Thaliana, CID - CISBAN Cross-Species Interactome Database, DRYGIN - Data Repository of Yeast Genetic INteractions, KNIFE - Drosophila pattern formation knowledge base, Mouse IDGenes - Gene interactions in the developing mouse brain, mutLBSgeneDB - mutated Ligand Binding Site gene DataBase, Predictive Networks - Predictive Networks, ABCdb - Archaea and Bacteria ABC Systems database, SCOPEC - Database of protein catalytic domains, SIMAP - The Similarity Matrix of Proteins, AANT - Amino Acid-Nucleotide Interaction Database, AARSDB - Aminoacyl-tRNA Synthetase Database, AtmiRNET - Reconstructing regulatory networks of Arabidopsis thaliana miRNAs, DGIdb - The Drug Gene Interaction Database, EpimiR - Curated Mutual Regulation between Epigenetic Modification and MiRNA, HCNet - Heart and Calcium Functional Network Database, iHOP - Information Hyperlinked Over Proteins, lncRInter - Database of long non-coding RNA interaction, LncRNA2Target - The lncRNA Target Gene Database, LncRNADisease - The LncRNA and Disease Database, lncRNASNP - A Database of Single Nucleotide Polymorphisms in long non-coding RNAs, microPIR - microRNA-promoter interactions resource, miRTarBase - The Experimentally Validated microRNA-target Interactions Database, NPIDB - Nucleic Acid-Protein Interaction Database, NPInter - Noncoding RNAs and protein related biomacromolecules interaction database, POSTAR - a platform of POST-trAnscriptional Regulation, Precise - Predicted and Consensus Interaction Sites in Enzymes, ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions, RAID v2 - RNA Association Interaction Database, SELEX_DB - Randomized DNA/RNA sequence database, sRNATarBase - sRNA-Target Interactions in Bacteria, TCDB - Transporter Classification Database, ViRBase - Virus-Host ncRNA Interaction Database, VIRmiRNA - Resource for Experimental Viral miRNA and their Targets, Transcription Factors / Gene Regulatory Networks.