Pathguide: the pathway resource list
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Full Record: Reactome  
Short NameReactome
Full NameReactome KnowledgeBase
Last ObservedFebruary 24th, 2017
DescriptionReactome is an open-source, curated database of human biological pathways, authored by expert biologists in collaboration with Reactome staff and peer-reviewed. Reactome's rationale is to convey the expert consensus view supported by information contained in the literature in a reusable, computationally accessible format. The core unit of Reactome's data model is the reaction, which encompasses all events in biology that change the state of a biological molecule. Binding, activation, translocation, degradation and classical biochemical catalysis events are all included. Reactions connect to form pathways. Reactome pathways cover a diverse range of biology including signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism. Curated human pathways are used to infer orthologous events in 20 non-human species including mouse, rat, chicken, worm, fly, yeast, plants and bacteria.

The Reactome website includes a pathway browser and a suite of data analysis tools to support pathway-based analysis of experimental data. Pathways are represented graphically using a Systems Biology Graphical Notation (SBGN)-based representation, with zooming, scrolling and event highlighting capabilities. PSICQUIC web services can be used to overlay molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, ChEMBL, BioGRID and iRefIndex. Reactome software and data are freely available for download in multiple formats including MySQL, BioPAX, SBML and PSI-MITAB. Data is also accessible through our Web Services APIs.
Sample Data URL 
Data SourcePrimary
AvailabilityFree to all users
PubMed ArticlesReactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome Biol. 2007;8(3):R39.

Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.
Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22.

Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L
Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7.

Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters.
Jassal B.
Hum Genomics. 2011 May;5(4):310-5.

Reactome pathway analysis to enrich biological discovery in proteomics data sets.
Haw R, Hermjakob H, D'Eustachio P, Stein L.
Proteomics. 2011 Sep;11(18):3598-613.

New gene functions in megakaryopoiesis and platelet formation.
Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y, Lopez LM, Magi R, Meacham S, Okada Y, Pirastu N, Sorice R, Teumer A, Voss K, Zhang W, Ramirez-Solis R, Bis JC, Ellinghaus D, Gogele M, Hottenga JJ, Langenberg C, Kovacs P, O'Reilly PF, Shin SY, Esko T, Hartiala J, Kanoni S, Murgia F, Parsa A, Stephens J, van der Harst P, Ellen van der Schoot C, Allayee H, Attwood A, Balkau B, Bastardot F, Basu S, Baumeister SE, Biino G, Bomba L, Bonnefond A, Cambien F, Chambers JC, Cucca F, D'Adamo P, Davies G, de Boer RA, de Geus EJ, Doring A, Elliott P, Erdmann J, Evans DM, Falchi M, Feng W, Folsom AR, Frazer IH, Gibson QD, Glazer NL, Hammond C, Hartikainen AL, Heckbert SR, Hengstenberg C, Hersch M, Illig T, Loos RJ, Jolley J, Khaw KT, Kuhnel B, Kyrtsonis MC, Lagou V, Lloyd-Jones H, Lumley T, Mangino M, Maschio A, Mateo Leach I, McKnight B, Memari Y, Mitchell BD, Montgomery GW, Nakamura Y, Nauck M, Navis G, Nothlings U, Nolte IM, Porteous DJ, Pouta A, Pramstaller PP, Pullat J, Ring SM, Rotter JI, Ruggiero D, Ruokonen A, Sala C, Samani NJ, Sambrook J, Schlessinger D, Schreiber S, Schunkert H, Scott J, Smith NL, Snieder H, Starr JM, Stumvoll M, Takahashi A, Tang WH, Taylor K, Tenesa A, Lay Thein S, Tonjes A, Uda M, Ulivi S, van Veldhuisen DJ, Visscher PM, Volker U, Wichmann HE, Wiggins KL, Willemsen G, Yang TP, Hua Zhao J, Zitting P, Bradley JR, Dedoussis GV, Gasparini P, Hazen SL, Metspalu A, Pirastu M, Shuldiner AR, Joost van Pelt L, Zwaginga JJ, Boomsma DI, Deary IJ, Franke A, Froguel P, Ganesh SK, Jarvelin MR, Martin NG, Meisinger C, Psaty BM, Spector TD, Wareham NJ, Akkerman JW, Ciullo M, Deloukas P, Greinacher A, Jupe S, Kamatani N, Khadake J, Kooner JS, Penninger J, Prokopenko I, Stemple D, Toniolo D, Wernisch L, Sanna S, Hicks AA, Rendon A, Ferreira MA, Ouwehand WH, Soranzo N.
Nature. 2011 Nov 30;480(7376):201-8.

Using the reactome database.
Haw R, Stein L
Curr Protoc Bioinformatics. 2012 Jun;Chapter 8:Unit8.7.

A network module-based method for identifying cancer prognostic signatures.
Wu G, Stein L.
Genome Biol. 2012 Dec 10;13(12):R112.

Pathway databases: making chemical and biological sense of the genomic data flood.
D'Eustachio P.
Chem Biol. 2013 May 23;20(5):629-35.

Building models using reactome pathways as templates.
Croft D.
Methods Mol Biol. 2013;1021:273-83.

The Reactome pathway knowledgebase.
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.
Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7.

The Reactome pathway Knowledgebase.
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.
Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7.

Types of DataMetabolic Pathways, Signaling Pathways, Pathway Diagrams
Types of ToolsPathway discovery tools
Small Molecules: 1,763
Genes / Proteins: 131,488
Interactions / Reactions: 84,759
Pathways: 22,928
Experiments / PubMed IDs: 26,859
Last Content Update: July 5th, 2017
Major OrganismsHomo sapiens
Relative Popularity1160
Homepage Uptime StatisticsWebsite tracker - uptime monitoring service
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"Pathguide: the pathway resource list" is maintained by Gary Bader1.
The website was originally created by Michael Cary 2 and was significantly updated and redesigned by Vuk Pavlovic1.
Thanks to Emek Demir for the Pathguide name.

1. Bader Lab
2. Sander Group

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