Reactome: A Curated Pathway Database

Resource Page

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. We are working on a second table that will provide an at-a-glance summary and will be grouped by themes.

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.

NameDescription
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.
AsteriasAsterias includes applications for the analysis of genomic and proteomic data that cover from data normalization to development of prediction models for survival data.
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.
BabelomicsBabelomics is a complete suite of web tools for the analysis, integration and interpretation of different types of genomic data.
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).
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.
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.
BioProfiling.deBioProfiling.de provides a common interface for a collection of recently developed analytical tools for genomics, proteomics and metabolimics data.
BioWisdom SRSBioWisdom Sequence Retrival System (SRS) is a proven and scalable data integration platform delivering genomic data to thousands of users.
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.
CANGESCANGES provides a means to rapidly identify networks for any set of genes and generate novel hypotheses.
CancerResourceCancerResource is a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge.
CCDBCell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle.
CellDesignerCellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks.
Cell IllustratorCell Illustrator is an enviroment for simulating and representing biological systems.
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.
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.
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.
CTDThe Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health.
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.
COFECOCOFECO is a web-based tool for a composite annotation of protein complexes.
cPathcPath is an open source pathway database and software suite designed for systems biology research.
CytoscapeCytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks.
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.
dbOGAPdbOGAP is a Database of O-GlcNAcylated Proteins and Sites.
DDECDragon Database of genes implicated in Esophageal Cancer (DDEC) is an integrated knowledge database aimed at representing a gateway to esophageal cancer related data.
DDPCDragon Database of Genes associated with Prostate Cancer (DDPC) is an integrated knowledge database aimed at representing a gateway to prostate cancer related data.
DICSThe DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network.
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 analysis and visualization.
ENFINENFIN is a network to enhance integrative systems biology.
Eu.Gene AnalyzerEu.Gene Analyzer is a tool for integrating gene expression data with pathway databases.
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.
FlyMineFlyMine is an integrated database for Drosophila and Anopheles genomics.
FlyReactomeFlyReactome is a curated knowledgebase of Drosophila melanogaster pathways.
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.
GATEGrid Analysis of Time-series Expression (GATE) ia an integrated computational software platform for the analysis and visualization of high-dimensional bio-molecular time-series.
GBMBaseGBMBase focuses on data used in Glioblastoma multiforme (GBM) research.
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.
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.
GeneSpringGeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data.
GenWay Biotech, Inc.GenWay Biotech, Inc. is a protein, antibody and ELISA solutions provider.
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.
GOMinerGoMiner™ is a tool for biological interpretation of 'omic' data – including data from gene expression microarrays.
GraphWebGraphWeb is a public web server for graph-based analysis of biological networks.
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.
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
HMDBThe Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.
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.
HMTDHuman Membrane Transporter Database
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
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.
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
INOHIntegrating Network Objects with Hierarchies (INOH) is a pathway database of model organisms including human, mouse, rat and others.
Linked Life DataLinked Life Data is a semantic integration platform for the biomedical domain.
KOBAS 2.0KOBAS 2.0 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.
METANNOGENMETANNOGEN is a flexible tool to manage information for the design of metabolic networks.
METACYCMetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways.
metaTIGERmetaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes.
MiMIMichigan Molecular Interactions (MiMI) provides access to the knowledge and data merged and integrated from numerous protein interactions databases.
MINTMINT is a public repository for molecular interaction data.
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.
mirDIPmicroRNA Data Integration Portal (mirDIP) integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches.
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.
MyBiosourceMyBiosource is a provider of antibody, protein, peptide and ELISA reagents.
NCBI BioSystemsThe NCBI Biosystems database centralizes and cross-links existing biological systems databases.
NCBI Entrez 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.
ncRNAncRNA is a portal site for bioinformatics tools and databases spcialized for functional RNAs.
NetBoxNetBox is a Java-based software tool for performing network analysis on human interaction networks.
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.
NetWORKINNetWORKIN is a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins.
neXtProtneXtProt is a human-centric discovery platform offering its users a seamless integration of and navigation through proteins-related data.
p53 KnowledgebaseThe p53 Knowledgebase isan integrated information resource for p53 research
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.
PathJamPathJam is a public tool which provides an intuitive and user-friendly framework for biological pathway analysis of human gene lists.
PathScanPathScan is Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes.
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.
PATIKAwebPathway Analysis Tool for Integration and Knowledge Acquisition
PharmGKBIntegrated data resource about how variation in human genetics leads to variation in response to drugs.
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.
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.
PRIDEThe Proteomics Identifications database at EBI is a mass spectrometry-derived proteomics data repository.
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.
PROProtein Ontology (PRO) is a formal representation of protein objects, providing both descriptions of these objects and the relationships between them
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.
PyBioSPyBioS is a system for the modeling and simulation of cellular processes.
RDFScapeRDFScape is a plugin that has been developed to to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.
ReConnReConn is a Java plugin that connects Cytoscape to the Reactome database.
RGDRat Genome Database (RGD) is a collection of genetic and genomic information on the rat.
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.
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.
SBMLThe Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes.
SciMinerSciMiner is a dictionary- and rule-based biomedical literature mining and functional enrichment analysis tool.
SIDEKICKSIDEKICK is a genomic data driven analysis and decision-making framework.
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.
SignaLinkSignaLink allows system-level analyses using the network of the major intracellular signaling pathways.
SimBiology 3.1SimBiology® provides graphical and programmatic tools for computational systems biology and pharmacokinetics.
SMPDBThe Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans.
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.
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.
STITCHSTITCH is an interaction network database for small molecules and proteins.
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.
T1DBaseT1DBase focuses on two research areas in type 1 diabetes (T1D): the 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.
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.
The Cell Cycle OntologyThe Cell Cycle Ontology is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process.
ToppgeneToppgene Suite is an one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network.
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.
VeryGeneVeryGene serves as a tissue-specific genes knowledgebase and a discovery tool to generate testable hypotheses for basic and clinical research.
visANTvisANT is an integrative visual analysis tool for biologucal networjs and pathways.
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).
VisHiCVisHiC is a public web server for clustering and interpreting gene expression data.
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.
WikiPathwaysWikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community.
WormBaseWormBase is a central data repository for nematode biology.