Reactome: A Curated Pathway Database

Resource Guide

Here we provide information regarding software tools, websites, databases and research projects that support Reactome data, use the Reactome data model, or link to the Reactome website. The table provides a list of the resources, a brief description of each resource and a linking URL.

If we are missing your website, database, software tool and project, please use the Survey to notify us about additions and suggestions. Alternatively, you can contact Robin Haw thorough our HelpDesk.

ABACUSABACUS is an Algorithm based on a BivAriate CUmulative Statistic to identify single nucleotide polymorphisms (SNPs) significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions
AbsIDconvertAbsIDconvert is an absolute approach for converting genetic identifiers at different granularities
ADaCGHADaCGH is a parallelized web-based application and R package for the analysis of aCGH data
AgBaseAgBase is a functional genomics resource for agriculture
Algal Functional Annotation ToolAlgal Functional Annotation Tool is a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
AltAnalyzeAltAnalyze is a platform for analyzing and visualizing exon expression data
AMMO_ProtAMMO-Prot is an amine system project 3D-model finder
Annotate-itAnnotate-it is a Swiss-knife approach to annotation, analys is and interpretation of single nucleotide variation in human disease
Arabidopsis ReactomeArabidopsis Reactome is a curated knowledgebase of plant biological pathways that contains many plant pathways curated by the John Innes Centre team, plus plant pathways imported from AraCyc and KEGG
ARACNeARACne is an Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
AsteriasAsterias includes applications for the analysis of genomic and proteomic data that cover from data normalization to development of prediction models for survival data
atBioNetatBioNet is an integrated network analysis tool for genomics and biomarker discovery
Atlas of Genetics and Cytogenetics in Oncology and HaematologyThe Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal and database in free access on internet devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases
AutismKBAn evidence-based knowledgebase of autism genetics
BabelomicsBabelomics is a complete suite of web tools for the analysis, integration and interpretation of different types of genomic data
Baysian Pathway AnalysisA computational method to identify significant pathways from microarray data with samples from test and control classes
BcClusterBcCluster is a Bladder Cancer Database at the Molecular Level
BCMLThe biological Connection Markup Language is a SBGN-compliant format for visualization, filtering and analysis of biological pathways
BIANABiological interactions and network analysis (BIANCA) is a software framework for compiling biological interactions and analyzing networks
BindingDBA public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules
BiNoMBiological Network Manager is a Cytoscape plug-in, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX)
Bio3graphAutomated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts
BioBinBioBin is a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge
BioDBBioDB is an ontology-enhanced information system for heterogeneous biological information
BioDWHBioDWH is a Data Warehouse Kit for Life Science Data Integration
BiofilterBiofilter is a knowledge-integration system for the multi-locus analysis of genome-wide association studies
biofilter 2.0A single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of Library of Knowledge Integration (LOKI)
BioGPSBioGPS is a free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function
BioGRIDThe Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species
BioHealthBase BRCBioHealthBase Bioinformatics Resource Center (BRC) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens-Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin
BioJSBioJS is an open source standard for biological visualisation
BiologicalNetworksData integration and network based research environment with tools for inference and analysis of gene regulatory modules
BioMartBioMart enables scientists to perform advanced querying of biological data sources through a single web interface
BioMobyBioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services
BioModelsBioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests
BioMynBioMyn is an integrated human gene and protein knowledgebase
BioPAXBiological Pathway Exchange (BioPAX) is a RDF/OWL-based standard for the exchange of biological pathways
BioPAX Cytoscape PlugInBioPAX Cytoscape PlugIn enables Cytoscape users to load and visually render BioPAX files from the web or a local file system; distributed with Reactome sample files
BioPPBioPP is a tool for web-publication of biological networks
BioProfiling.deBioProfiling de provides a common interface for a collection of recently developed analytical tools for genomics, proteomics and metabolimics data
BioSemanticBioSemantic is a framework that was designed to speed integration ofrelational biological databases
BiovistaSystematic drug repositioning capability offers decision makers a reliable tool for pipeline optimization, asset protection and life cycle management
BioWisdom SRSBioWisdom Sequence Retrival System (SRS) is a proven and scalable data integration platform delivering genomic data to thousands of users
BirdsEyeViewVisualizing experimental transcriptomic data using different views that users can switch among and compare
BirdsEyeViewBirdsEyeView (BEV) is agraphical overviews of experimental data
BisoGenetBisoGenet is a Cytsocape app for gene network building, visualization and analysis
BNPBayesian Network Prior (BNP) depicts the relation between various evidence types that contribute to the event gene interaction and is used to calculate the probability of a candidate graph (G) in the structure learning process
BowTieBuilderBowTieBuilder is aModeling signal transduction pathways
C2Cards - HumanConsensus and Conflict Cards (C2Cards) provides concise overviews of what pathway databases do or do not agree on
caBIGcancer Biomedical Informatics Grid¬ caBIG¬ is an information network enabling all constituencies in the cancer community _ researchers, physicians, and patients _ to share data and knowledge
CAERUSCAERUS predicts CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data
CancerResourceCancerResource is a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
CANGESCANGES provides a means to rapidly identify networks for any set of genes and generate novel hypotheses
canSARcanSAR is an integrated cancer public translational research and drug discovery resource
CardioNetA human metabolic network suited for the study of cardiomyocyte metabolism
CardioNetCardioNet is a human metabolic network suited for the study of cardiomyocyte metabolism
CardioVINEdbCardioVINEdb is adata warehouse approach for integration of life science data in cardiovascular diseases
CCDBCell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle
CEGPCancer Gene Encyclopedia will allow scientists to identify new cancer targets
Cell Cycle OntologyThe Cell Cycle Ontology is an application ontology for the representation and integrated analysis of the cell cycle process
Cell IllustratorCell Illustrator is an enviroment for simulating and representing biological systems
CellBaseCellBase is a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources
CellCircuitsCellCircuits is a database of protein network models
CellDesignerCellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks
CellFrameCellFrame is a data structure for abstraction of cell biology experiments and construction of perturbation networks
Characterization ToolThe Characterization Tool is a novel knowledge-based database and web application that allows the storage and analysis of various kinds of data associated with cell, cell line and tissue characterization across different species
ChEBIChemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds
Chem2Bio2RDFChem2Bio2RDF is a semantic framework for linking and data mining chemogenomic and systems chemical biology data
ChemProtChemPort is a disease chemical biology database, which is based on a compilation of multiple chemical_protein annotation resources, as well as disease-associated protein_ protein interactions
ChiBEChisio BioPAX Editor (ChiBE) is a free editing and visualization tool for pathway models represented by the BioPAX format
ChipsterChipster is a user-friendly analysis software for microarray and other high-throughput data
CIDeRCIDeR is aMultifactorial interaction networks in human diseases
CIDMSCardiac Integrated Database Management System (CIDMS) integrates the heterogeneous -omic data (available from multitude of sources and in various formats such as publication and associated supplementary files, databases and web pages) that are generated at different biological levels
CluepediaCluePedia provides insights into pathways by integrating experimental and in silico information
CMSA Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers
COFECOCOFECO is a web-based tool for a composite annotation of protein complexes
ConsensusPathDBConsensusPathDB is a database system for the integration of human functional interactions
COPASICOPASI is a software application for simulation and analysis of biochemical networks and their dynamics
cPathcPath is an open source pathway database and software suite designed for systems biology research
CPNMContext-specific Protein Network Miner derives context-specific PPI networks in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system
CSAXCharacterizing Systematic Anomalies in eXpression Data (CSAX) aids in both identifying anomalies and explaining the underlying biology in expression datasets
CTDThe Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health
CTSA Pharmaceutical Assests PortalThe Pharmaceutical Assets Portal aims to facilitate industry-academic collaborations for discovery of new indications for compounds no longer being developed by pharmaceutical companies, through eliminating barriers to access such compounds
CyTargetLinkerA Cytoscape App to Integrate Regulatory Interactions in Network Analysis
CytoscapeCytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks
DAPDDAPD is a knowledgebase for Diabetes Associated Proteins
DAPPERDAPPER is a data-mining resource for protein-protein interactions
DAPPLEDisease Association Protein-Protein Link Evaluator (DAPPLE) looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature
DAVIDDatabase for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes
DawnRankDawnRank is a discover tool for personalized driver genes in cancer
dbOGAPdbOGAP is a Database of O-GlcNAcylated Proteins and Sites
DC-ATLASDC-ATLAS is a systems biology resource to dissect receptor specific signal transduction in dendritic cells
DDECDragon Database of genes implicated in Esophageal Cancer (DDEC) is an integrated knowledge database aimed at representing a gateway to esophageal cancer related data
DDESCDDESC is Dragon database for exploration of sodium channels in humans,
DDPCDragon Database of Genes associated with Prostate Cancer (DDPC) is an integrated knowledge database aimed at representing a gateway to prostate cancer related data
DECODEDECODE is an integrated differential co-expression and differential expression analysis of gene expression data
DeDaLDeDaL is a Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts
DEEPDEEP is a tool for differential expression effector prediction
DESHCVDragon Exploratory System on Hepatitis C Virus (DESHCV) is a biomedical text-mining and relationship exploring knowledgebase is the first reported comprehensive Hepatitis C Virus (HCV)
DESSCDDragon Exploration System for Sickle Cell Disease permits the exploration of text-mined and data-mined information about SCD
DESTAFDragon Exploration System for Toxicants and Fertility (DESTAF) is a specialized, public resource specifically aimed at researchers investigating reproductive toxicity
DICSThe DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network
DintorDintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets
Discovery-2An interactive resource for the rational selection and comparison of putative drug target proteins in malaria Phelelani T
DisGeneNetDisGeNET is a discovery platform integrating information on gene-disease associations (GDAs) from several public data sources and the literature
DNAtrafficDNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life
DR-GASDR-GAS is a database of functional genetic variants and their phosphorylation states in human DNA repair systems
DriverDB:DriverDB is an exome sequencing database for cancer driver gene identification
DriverNetDriverNet is auncovering the impact of somatic driver mutations on transcriptional networks in cancer
DroIDDrosophila Interactions Database is a comprehensive resource for annotated gene and protein interactions
DrugVizDrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome
DRYGINData Repository of Yeast Genetic Interactions (DRYGIN) is a web database system that provides a central platform for yeast genetic network analys is and visualization
ECMDBECMDB is The E coli Metabolome Database
EDdbEddb is a web resource for eating disorder and its application to identify an extended adipocytokine signaling pathway related to eating disorder
EndoNetEndoNet is an information resource about the intercellular signaling network
ENFINENFIN is a network to enhance integrative systems biology
Enrichment mapEnrichment map is a network-based method for gene-set enrichment visualization and interpretation
EnrichrEnrichr is an Interactive and collaborative HTML5 gene list enrichment analysis tool
Enzyme PortalMines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature
Eu.Gene AnalyzerEu Gene Analyzer is a tool for integrating gene expression data with pathway databases
ExpanderEXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use
ExPASy Proteomics ServerExpert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
FACTFACT is a framework for the functional interpretation of high-throughput experiments
FLIGHTFLIGHT an online resource compiling data from over 100 Drosophila in vivo and in vitro RNAi screens
FluMapComprehensive pathway map that can serve as a graphically presented knowledgebase and as a platform to analyze functional interactions between IAV and host factors
FluxMapA VANTED add-on for the visual exploration of flux distributions in biological networks
FlyMineFlyMine is an integrated database for Drosophila and Anopheles genomics
FlyReactomeFlyReactome is a curated knowledgebase of Drosophila melanogaster pathways
fugaFunctional Genomics Assistant is an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics
FunGenESThe FunGenES database is a genomics resource for mouse embryonic stem cell differentiation
g:Profilerg:Profiler is a web-based toolset for functional profiling of gene lists from large-scale experiments
G2SBCGenes-to-Systems Breast Cancer (G2SBC) Database is a bioinformatics resource that collects and integrates data about genes, transcripts and proteins which have been reported in literature to be altered in breast cancer cells
GaggleGaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data
Gallus Genome GBrowseGallus Genome GBrowse provides online access to genomic and other information about the chicken
GallusReactomeGallusReactome is a curated knowledgebase of chicken pathways
GANPAA novel gene-weighed pathway analys is approach, as implemented in an R package called ñGene Associaqtion Network-based Pathway Analysis"
GAPGene functional Association Predictor is an integrative method for predicting and characterizing gene functional associations
GATEGrid Analysis of Time-series Expression (GATE) ia an integrated computational software platform for the analys is and visualization of high-dimensional bio-molecular time-series
GBMBaseGBMBase focuses on data used in Glioblastoma multiforme (GBM) research
GCMAPGCMAP is a user-friendly connectivity mapping with R
GEDIGenetic Diseases Gene Discovery (GEDI) provides integrated bioinformatics platforms that will support systems analysis of Human multigene disorders
Gene OntologyThe Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases
Gene3DGene3D is a domain-based resource for comparative genomics, functional annotation and protein network analysis
GeneAnswersUsing the Bioconductor GeneAnswers Package to Interpret Gene Lists
GeneBrowser 2GeneBrowser 2 is an application to explore and identify common biological traits in a set of genes
GeneCardsExtracts and integrates gene-related data, including genomic, transcriptomic, proteomic, genetic, clinical, and functional information
GeneMANIAHelps you predict the function of your favourite genes and gene sets
GeneSigDBGeneSigDB is a manually curated database and resource for analysis of gene expression signatures
GeneSpringGeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data
GeneSrFGeneSrF is a web-based tool for gene selection and classification using random forest
GeneTrail 2GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures
GenMAPPGene Map Annotator and Pathway Profiler (GenMAPP) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signaling), connecting gene-level datasets to biological processes and disease
GenomeSpaceA cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface
GenWay Biotech, Inc.GenWay Biotech, Inc is a protein, antibody and ELISA solutions provider
gespeRgespeR is a statistical model for deconvoluting off-target-confounded RNA interference screens
GEYSIRGenomic Explorer Y Survey of Immune Response (GEYSIR) is a web application designed to correlate case-control association data with genetic and physical maps of the human genome, including key human genes associated with host immune response
GingerSNPGingerSNP tools help you explore standard human SNP arrays by interaction, pathway, and function
GLAMMGLAMM is a Genome-Linked Application for Metabolic Maps
GOALGOAL is a software tool for assessing biological significance of genes groups
GOMinerGoMiner» is a tool for biological interpretation of 'omic' data _ including data from gene expression microarrays
GPECGPEC is a Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection
graphiteA Bioconductor package to convert pathway topology to gene network
GraphWebGraphWeb is a public web server for graph-based analysis of biological networks
GSEAGene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states
GuavaHGuavaH is a compendium of host genomic data in HIV biology and disease
HAPMAPThe International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals
HCVproHCVpro is a Hepatitis C virus protein interaction database
HDAPDHDAPD is a web tool for searching the disease-associated protein structures
HEFalMpHEFalMp (Human Experimental/FunctionAL MaPper) is a tool that allows interactive exploration of functional maps (or functional relationship networks) predicted from integration of many genome-scale experimental results
HepatoNet1HepatoNet1 is a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
HGNCThe HGNC database in 2008 is a resource for the human genome
hiPathDBhiPathDB is a human-integrated pathway database with facile visualization
hLGDBhLGDB is a database of human lysosomal genes and their regulation
HMDBThe Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body
HMPASHuman Membrane Protein Analysis System provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups
HMPASHMPAS is a Human Membrane Protein Analysis System
HMTDHuman Membrane Transporter Database
HOCCLUS2bicluster miRNAs and target messenger RNAs (mRNAs) on the basis of their experimentally-verified and/or predicted interactions
HomoMINTHomoMINT is an inferred human network based on orthology mapping of protein interactions discovered in model organisms
HPDHuman Pathway Database (HPD) is an integrated human pathway database providing comprehensive and combined view connecting human proteins, genes, RNAs, enzymes, signaling, metabolic reactions and gene regulatory events
HPIDBHPIDB is a unified resource for host-pathogen interactions
HubbaHubba is ahub objects analyzer--a framework of interactome hubs identification for network biology
HuPhoHuPho is a human phosphatase portal
IBDsiteA disease-oriented platform, which collects data related to biomolecular mechanisms involved in the Inflammatory Bowel Disease onset
IDClightIDClight converts single IDs through an URL
IdconverterIdconvertor map IDs to other known public DBs
ImmPortImmunology Database and Analysis Portal (ImmPort), is a one stop shop to access reference and experiment data for immunologists
Influenza Research DatabaseInfluenza Research Database is a resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism
InnateDBInnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection
INOHIntegrating Network Objects with Hierarchies (INOH) is a pathway database of model organisms including human, mouse, rat and others
INRICHNRICH is an Interval-based Enrichment Analysis Tool for Genome Wide Association Studies
IntActIntAct is an open source resource for molecular interaction data
IntegromeDBIntegromeDB is an integrated system and biological search engine
Interactome3DA resource for the structural annotation and modeling of protein-protein interactions
IntermineAn open source data warehouse built specifically for the integration and analysis of complex biological data
IPADIntegrated Pathway Analysis Database for Systematic Enrichment Analysis for defining inter-association between pathway, disease, drug and organ specificity
iPASiPAS is series of integrative steps, which extend existing pathway analysis techniques It consists of four parts is adata processing, gene-level statistics, individualized pathway aberrance score (iPAS) and a significance test
IPAVSIPAVS is aIntegrated Pathway Resources, Analys is and Visualization System
ISAACInterSpecies Analysing Application using Containers is a web based tool, which analyses sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis
KaBOBKaBOB is an ontology-based semantic integration of biomedical databases
KDBIUpdate of KDBI is a Kinetic data of bio-molecular interaction database
KeyPathwayMinerKeyPathwayMiner is a condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape
KOBAS 2.0KOBAS is an update of KOBAS (KEGG Orthology Based Annotation System) Its purpose is to identify statistically enriched related pathways and diseases for a set of genes or proteins, using pathway and disease knowledge from multiple commonly used databases
LDGIdbLDGIdb is a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs
Linked Life DataLinked Life Data is a semantic integration platform for the biomedical domain
LipidHomeA Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
Lists2NetworksLists2Networks provides integrated analysis of gene/protein lists
LiverAtlasLiverAtlas is a unique integrated knowledge database for systems-level research of liver and hepatic disease
LOKILibrary of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data
MAGeCKMAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
ManteiaManteia is a predictive data mining system for vertebrate genes and its applications to human genetic diseases
mAPKLmAPKL is aR/Bioconductor package for detecting gene exemplars and revealing their characteristics
MassVisMassVis is aVisual analysis of protein complexes using mass spectrometry
MeSHMeSH ORA framework is aR/Bioconductor packages to support MeSH over-representation analysis
Meta-AllMeta-All is a system for managing metabolic pathway information
MetaboLightsThe MetaboLights repository is aCuration challenges in metabolomics
MetaCropMetaCrop 20 is amanaging and exploring information about crop plant metabolism
METACYCMetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways
MetaMappMapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
METANNOGENMETANNOGEN is a flexible tool to manage information for the design of metabolic networks
MetaRegMetaReg is a platform for modeling, analys is and visualization of biological systems using large-scale experimental data
metaTIGERmetaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes
MetNet OnlineMetNet Online is a novel integrated resource for plant systems biology
MetNetAPIMetNetAPI is a flexible method to access and manipulate biological network data from MetNet
MetRxnMetRxn is a knowledgebase of metabolites and reactions spanning metabolic models and databases
MGVMGV is a generic graph viewer for comparative omics data
MiMIMichigan Molecular Interactions (MiMI) provides access to the knowledge and data merged and integrated from numerous protein interactions databases
MIMOMIMO is an efficient tool for molecular interaction maps overlap
MimozaMimoza is a web-based semantic zooming and navigation in metabolic networks
MINTMINT is a public repository for molecular interaction data
mirDIPmicroRNA Data Integration Portal (mirDIP) integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches
MIRIAMMIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology
miRror-SuitemiRror-Suite platform provides a concise, plausible explanation for the regulation of miRNAs in such complex settings
miRSystemmiRSystem is an Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets
MK4MDDMK4MDD is a Multi-Level Knowledge Base and Analysis Platform for Major Depressive Disorder
MMMDBMMMDB is a Mouse Multiple Tissue Metabolome Database
modMinemodMine is a flexible access to modENCODE data
MODOMICSMODOMICS is a database of RNA modification pathways - 2013 update
MoKCaThe MoKCa (Mutations of Kinases in Cancer) database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer
MoonDBMoonDB is a database containing information on all the candidates identified in the analys is and a set of manually curated human moonlighting proteins
MOPEDModel Orgnaism Protein Expression Database enables discoveries through consistently processed proteomics data
MSigDBThe Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software
MuSiCMuSiC is an Identifying mutational significance in cancer genomes
MyBiosourceMyBiosource is a provider of antibody, protein, peptide and ELISA reagents
NaviCellNaviCell is a web-based environment for navigation, curation and maintenance of large molecular interaction maps
NAViGaTORA powerful graphing application for the 2D and 3D visualization of biological networks
NCBI BioSystemsThe NCBI Biosystems database centralizes and cross-links existing biological systems databases
NCBI GeneEntrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer
NCBO BioportalBioPortal is a Web-based application for accessing and sharing biomedical ontologies
NCISNCIS is a Network-assisted Co-clustering for the Identification of cancer Subtypes
ncRNAncRNA is a portal site for bioinformatics tools and databases spcialized for functional RNAs
NeMoNeMo is a Network Module identification in Cytoscape
NetBoxNetBox is a Java-based software tool for performing network analysis on human interaction networks
NetHiKeA simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network
NetPathNetPath is a public resource of curated signal transduction pathways
NetSlimNetSlim is a High-confidence curated signaling maps
NetWalkerNetWalker is a contextual network analysis tool for functional genomics
NetworkNetwork Screening is a New Method to Identify Active Networks from an Ensemble of Known Networks
Network2CanvasNetwork2Canvas is a Network Visualization on a Canvas with Enrichment Analysis
NetWORKINNetWORKIN is a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins
NetworkLegoNetworkLego is a general computational framework for detecting cellular networks that are activated in a particular cell state or in response to a perturbation and for determining core cellular networks that are activated in response to multiple perturbations
NetworkPrioritizerA versatile tool for network-based prioritization of candidate disease genes or other molecules
NeuroDNetAn open source platform for constructing and analyzing neurodegenerative disease networks
neXtProtneXtProt is a human-centric discovery platform offering its users a seamless integration of and navigation through proteins-related data
NGPNetworked Gene Prioritizer integrates gene expression and protein-protein interaction network to prioritize cancer-associated genes
OncoRepOncoRep is an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Onto-ToolsOnto-Tools is a New additions and improvements in 2006
OntoSlugOntoSlug is a dynamic visual front-end program for ontologies
OPHIDIntegrated known, experimental and predicted PPIs for five model organisms and human in the I2D database
ORCIDORCID provides a persistent digital identifier that distinguishes you from every other researcher
OREMPdbOntology Reasoning Engine for Molecular Pathways is a semantic dictionary of computational pathway models
p53 KnowledgebaseThe p53 Knowledgebase isan integrated information resource for p53 research
PAGEDPAGED is a pathway and gene-set enrichment database to enable molecular phenotype discoveries
PAGERPAGER is a new database framework to perform integrative ñgene-set, network, and pathway analysisî (GNPA)
PaLSPaLS is a tool that filters, from a list or a set of lists of gene/clone/protein identifiers, those that meet certain criteria related to their references to articles in PubMed, Gene Ontology terms and KEGG and Reactome pathways
Pancreatic Expression databaseThe Pancreatic Expression database is the main repository for pancreatic-derived -omics data
PandoraPandora is a novel integrated approach that uses network topology to predict biological pathways
PARADIGM-SHIFTPARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
Path2ModelsPath2Models is a Large-scale generation of computational models from biochemical pathway maps
PathAgentPathAgent is a Multi-agent System for Updated Pathway Information Integration
PathCase-SBPathCase-SB is integrating data sources and providing tools for systems biology research
PathJamPathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists
PATHLOGIC-SA Scalable Boolean Framework for Modelling Cellular Signalling
PathNERPathway Named Entity Recognition is a tool for systematic identification of biological pathway mentions in the literature
PathprintingPathprinting is an integrative approach to understand the functional basis of disease
PathRingsPathRings is a web-based tool for exploration of ortholog and expression data in biological pathways
PathScanPathScan is Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes
PathVarPathVar is analysis of gene and protein expression variance in cellular pathways using microarray data
PathviewPathview is an R/Bioconductor package for pathway-based data integration and visualization
PathVisioRPCAutomatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Pathway ProjectorPathway projector is a Web-based zoomable pathway browser using KEGG Atlas and Google Maps API
Pathway CommonsPathway Commons provides researchers with convenient access to a comprehensive collection of pathways from multiple organisms
Pathway Interaction DatabasePathway Interaction Database (PID) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes
Pathway Knowledge BasePathway Knowledge Base is a public repository for searching biological pathways
Pathway-GPSPathway-GPS and SIGORA is aIdentifying relevant pathways based on the over-representation of their gene-pair signatures
PathwayCaseMAWPathwayCaseMAW is an online system for metabolic network analysis
PathwayLinkerA system of integrating protein-protein interaction and signaling pathway data from several sources with statistical significance tests and clear visualization
PATIKAmadPATIKAmad puts microarray data into pathway context
PATIKAwebPathway Analysis Tool for Integration and Knowledge Acquisition
PaxToolsAn open-source, Java library that contains facilities and algorithms for common but difficult to implement tasks such as reading, writing, searching, merging, comparing and transforming pathway information
PayaoPayao is a community platform for SBML pathway model curation
PBSK browserPBSK browser allows users to navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats
PDBAn Information Portal to Biological Macromolecular Structures
PDBeThe Protein Data Bank in Europe (PDBe) is abringing structure to biology
PDDBPrion Disease Database (PDDB) focuses on data used in Prion Disease (PD) research This site provides tools which allow scientists to analyze, store, and share this PD data with other scientists
PEANuTPathway enrichment analysis tool provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks
PENTACONThe Personalized NSAID Therapeutics Consortium (PENTACON) is a group of scientists with a wide range of expertise from multiple institutions whose collective aim is to develop a paradigm for the personalization of drug treatment
PharmGKBIntegrated data resource about how variation in human genetics leads to variation in response to drugs
PhosphoELMPhosphoELM is a database of phosphorylation sites - Update 2008
PIGPathogen Interaction Gateway is a database of host-pathogen PPI (HP-PPI) data from a number of public resources
PIRProtein Infromation Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies
PlantReactomeA freely accessible plant pathway database which hosts plant metabolic and regulatory pathways
PLAZAA Comparative Genomics Resource to Study Gene and Genome Evolution in Plants
PolyDomsPolyDoms is a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
Pomelo IIPomelo II is an open-source, web-based, freely available tool for the analysis of gene (and protein) expression and tissue array data
PosMedPositional MEDLINE (PosMed) prioritizes candidate genes for positional cloning
PpiTrimPpiTrim is for constructing non-redundant and up-to-date interactomes
Predicted Arabidopsis Interactome ResourceA database of potential plant interactions, detailed annotations and more specific per interaction confidence measurement
PRGdbPRGdb is a community-based database model for the analysis of R-genes in plants
PRIDEThe Proteomics Identifications database at EBI is a mass spectrometry-derived proteomics data repository
PrioritizerA prioritization method for positional candidate genes, by assuming that the majority of causative genes are functionally closely related
PROProtein Ontology (PRO) is a formal representation of protein objects, providing both descriptions of these objects and the relationships between them
PROGgeneV2PROGgeneV2 is a Pan Cancer Prognostics Database
ProKinOProKinO is a framework for protein kinase ontology
ProteomicProteomic atlas of the human olfactory bulb
PSI-MIThe HUPO Proteomics Standards Initiative Molecular Interaction (PSI-MI) workgroup defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification
PSIQUICPSIQUIC a web service to access the PSI-MI interaction data
pSTIINGpSTIING is a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
PUPPIPUPPI is a pathway analysis method using protein-protein interaction network for case-control data
PyBioSPyBioS is a system for the modeling and simulation of cellular processes
Quartz-SeqQuartz-Seq is a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
RDF2GraphRDF2Graph a tool to recover, understand and validate the ontology of an RDF resource
RDFScapeRDFScape is a plugin that has been developed to to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape
Reactome.dbA set of annotation maps for reactome assembled using data from Reactome
ReactomePAReactomePA is a R package for Reactome Pathway Analysis
ReConnReConn is a Java plugin that connects Cytoscape to the Reactome database
RefNetBuilderRefNetBuilder is a platform for construction of integrated reference gene regulatory networks from expressed sequence tags
Regulatory GenomicsA Database of Annotated Promoters of Genes Associated with Common Respiratory and Related Diseases
ReMatchReMatch is a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis
REPAIRtoireREPAIRtoire is a database of DNA repair pathways
RGDRat Genome Database (RGD) is a collection of genetic and genomic information on the rat
RheaRhea is a manually curated resource of biochemical reactions
RhesusBaseRhesusBase is a knowledgebase for the monkey research community
RMODA Tool for Regulatory Motif Detection in Signaling Network
RNApathwaysDBRNApathwaysDB is a database of RNA maturation and decay pathways
ROCKROCK is a breast cancer functional genomics resource
RspiderR spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the REACTOME and KEGG databases
RxnFinderRxnFinder is a Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
SABIO-RKSystem for the Analysis of Biochemical Pathways - Reaction Kinetics is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured
SAGASAGA is a subgraph matching tool for biological graphs
SASDSynthetic Alternative Splicing Database for identifying novel isoform from proteomics
SASDSASD is athe Synthetic Alternative Splicing Database for identifying novel isoform from proteomics
SB-KOMSB-KOM provides integration of pathway information using BioPax
SBGNSystems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes
SBKDThe Structural Biology Knowledgebase is a portal to protein structures, sequences, functions, and methods
SBMLThe Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes
SBML-BridgeSBML-Bridge is an XML Pathway Converting Tool
SciMinerSciMiner is a dictionary- and rule-based biomedical literature mining and functional enrichment analysis tool
SIDEKICKSIDEKICK is a genomic data driven analys is and decision-making framework
SigCSAn integrated genetic information resource for human cerebral stroke
SignaLinkSignaLink allows system-level analyses using the network of the major intracellular signaling pathways
SignalogsSignalogs is an Orthology-based identification of novel signaling pathway components in three metazoans
SignSSignS is a web tool for gene selection and signature finding in problems where the dependent variable is patient survival or, more generally, a right-censored variable
SimBiology 3.1SimBiology¬ provides graphical and programmatic tools for computational systems biology and pharmacokinetics
SIPPERSIPPER is a flexible method to integrate heterogeneous data into a metabolic network
SMARTSMART dipslays domains in the context of genomes and networks
SMPDBThe Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans
SNPrankerSNPranker is a gene-centric data mining tool for diseases associated SNP prioritization in GWAS
SOURCESOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports
SPARQLGraphSPARQLGraph is a web-based platform for graphically querying biological Semantic Web databases
SPIKESignaling Pathway Integrated Knowledge Engine is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray and other functional genomics data on interaction maps
SPIRESPIRE is a Systematic protein investigative research environment
StarBaseStarBase will decode miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
STITCHSTITCH is an interaction network database for small molecules and proteins
STRINGSTRING is global view on proteins and their functional interactions in 630 organisms
SuperTargetSuperTarget is an on drug-target interactions resource
SyBiLSystems Biology Linker is designed for visualizing pathway data files in BioPAX format, such as imported from Reactome and converting BioPAX file into SBML file
SZGRSZGR is a comprehensive schizophrenia gene resource
T1DBaseT1DBase focuses on two research areas in type 1 diabetes (T1D) is athe genetics of T1D susceptibility and beta cell biology
T2D-DbT2D-Db is a database of all molecular factors reported to be involved in the pathogenesis of Type 2 diabetes in human, mouse and rat
T2D@ZJUT2D@ZJU is a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus
T2DM-GeneMinerT2DM-GeneMiner is a web resource for analysing genes in relation to type 2 diabetes mellitus
TavernaTaverna Workbench is an open source tool for designing and executing workflows created by the myGrid project
TcoF-DBTcoF-DB is provide a comprehensive starting point for investigations into transcriptional regulation that include PPIs between Transcription Factors, Transcription Co-factors and other proteins
TEAKTEAK is a Topology Enrichment Analysis frameworK for detecting activated biological subpathways
The Cell CollectiveThe Cell Collective is an open and collaborative approach to systems biology
The Cell Cycle OntologyThe Cell Cycle Ontology is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process
TIMTIM (Tools to Input Models) is a tool which integrates biological objects and information about biological process modelling
ToppgeneToppgene Suite is an one-stop portal for gene list enrichment analys is and candidate gene prioritization based on functional annotations and protein interactions network
TranscriptomeBrowserTranscriptomeBrowser is aintroducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
TransDomainTransDomain is a transitive domain-based method in protein-protein interaction prediction
TRANSPATHTRANSPATH is an information resource for storing and visualizing signaling pathways and their pathological aberrations
tYNA platformThe tYNA platform for comparative interactomics is a web tool for managing, comparing and mining multiple networks
UCD 2D-PAGE DatabaseUCD 2D-PAGE Datavase is a Two-dimensional polyacrylamide gel electrophoresis database
UCSC Genome BrowserUCSC Genome Browser is an up-to-date source for genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations
UCSD-Nature Signaling GatewayThe UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction
UniHIThe Unified Human Interactome database provides researchers with a comprehensive platform to query and access human protein-protein interaction (PPI) data
UniProtKBThe UniProt Knowledgebase is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation
VANTEDVisualization and Analysis of Networks containing Experimental Data makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies
varSelRFvarSelRF is a R package for gene selection and classification using random forest
VeryGeneVeryGene serves as a tissue-specific genes knowledgebase and a discovery tool to generate testable hypotheses for basic and clinical research
viPErVirtual pathway explorer is a cytoscape app, which integrates _omics data with interactome data
VirHostNetVirHostNet (Virus-Host Network) is a knowledgebase system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains)
visANTvisANT is an integrative visual analysis tool for biologucal networjs and pathways
VisHiCVisHiC is a public web server for clustering and interpreting gene expression data
VorontoVoronto is a Mapper for expression data to ontologies
WAVeWAVe is a web analysis of the variome
Web ApolloWeb Apollo is a web-based genomic annotation editing platform
WhichGenesWhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources
Wiki-PiA Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function
WikiCellWikiCell is a unified resource platform for human transcriptomics research
WikiPathwaysWikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community
WIMWIM (Web Interfac for Modelling) is a tool which integrates biological objects and information about biological process modelling
WormBaseWormBase is a central data repository for nematode biology
YMDBYMDB is a yeast metabolome database
yOWLyOWL is an ontology-driven knowledge base for yeast biologists