Reactome knowledgebase of human biological pathways and processes

By L. Matthews, Gopal R. Gopinath, M. Gillespie, M. Caudy, David Croft, B. Bono, Phani V. Garapati, J. Hemish, H. Hermjakob, B. Jassal and 10 more. Nucleic Acids Res., 2008

972 citations recorded by the source corpus.

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms.

Subfields: Molecular Biology

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Citations in the corpus

Mutual exclusivity analysis identifies oncogenic network modules. (2012, background): “The first network, HRN1, is derived from Cerami et al. (2010), and consists of four curated data sources: Reactome (Matthews et al. 2009), the MSKCC Cancer Cell Map (Memorial Sloan-Kettering Cancer Center 2007), the NCI/ Nature Pathway Interaction Database (Schaefer et al. 2009), and the Human Prote”
g:Profiler—a web server for functional interpretation of gene lists (2011 update) (2011, positive): “Our automated interpretative analysis takes advantage of systematized knowledge about gene and protein function, including Gene Ontology (GO) (16), Human Phenotype Ontology (HPO) (17) and biological pathway databases KEGG (18) and Reactome (19).”
GeNGe: systematic generation of gene regulatory networks (2009, neutral): “, 2008), Reactome (Matthews et al., 2009), or ConsensusPathDB (Kamburov et al.”
Database resources of the National Center for Biotechnology Information (2011, methodology): “Currently Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (32–34), BioCyc (35), Reactome (36), the Pathway Interaction Database (37) and WikiPathways (38,39).”
ChemProt-3.0: a global chemical biology diseases mapping (2016, neutral): “OMIM (26), the human disease network (27) GeneCards (28), KEGG (29), Reactome (30), UniPathway (31) and Gene Ontology (32) databases were also downloaded, curated and included in our system.”
Database resources of the National Center for Biotechnology Information (2006, methodology): “Currently, Biosystems receives data from the Kyoto Encyclopedia of Genes and Genomes (35–37), BioCyc (38), Reactome (39), the Pathway Interaction Database (40), WikiPathways (41,42) and Gene Ontology (43).”
Pathway Commons, a web resource for biological pathway data (2010, methodology): “Pathway Commons collects data in the standard BioPAX format for biological pathway exchange (5).”
Substrate Fate in Activated Macrophages: A Comparison between Innate, Classic, and Alternative Activation (2010, methodology): “org/) to retrieve the REACTOME (19) pathways as gene sets.”
miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets (2012, methodology): “Five pathway databases, including Gene Ontology [26], KEGG [27], BioCarta, Pathway Interaction Database [28], and Reactome [29], were used to annotate the biological functions and canonical pathways of target genes.”
Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action (2012, background): “The list of relevant genes/proteins involved in these processes can be identified through the use of databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) (52), the Gene Ontology project (53), and Reactome (54), or the list may be manually curated on the basis of the physiology of int”
The NCBI BioSystems database (2009, methodology): “Fortunately, a considerable number of resources have been created to address this issue: the Pathguide (1) resource lists nearly 300 pathway resources alone, including KEGG (2), Reactome (3), PID (4), PharmGKB (5), GenMAPP (6), Biocyc (7) and many others.”
Chemical Entities of Biological Interest: an update (2009, methodology): “We have also extended our automatic crossreference links to include annotated ChEBI identifiers within the ArrayExpress (11), BioModels (12), Reactome (13) and SABIO-RK (14) databases.”
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 (2012, methodology): “(1) All chemicals that can be isolated from a living organism; (2) All metabolites (primary and secondary); (3) Secondary metabolites only; (4) Secondary metabolites in plants only.”
Molecular signatures database (MSigDB) 3.0 (2011, background): “RESULTS set collections: gene sets in MSigDB 3.0 are [including 430 new sets contributed by Reactome Matthews et al. , 2009)], and sets corresponding to chemical genetic perturbations from 786 scientiﬁc publications.”
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis (2011, methodology): “Other expansions to functional data sets include the addition of protein interactions from BIOGRID (20), Reactome (21) and DIP databases (22), to supplement the previous set which comprised of Intact (23), Mint (24) and HPRD (25).”