title: The Reactome pathway Knowledgebase.
abstract: The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Antonio
authors.initials: A
authors.lastname: Fabregat
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Sidiropoulos
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Phani
authors.initials: P
authors.lastname: Garapati
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada College of Pharmacy and Health Sciences, St John's University, Queens, NY 11439, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Gillespie
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Hausmann
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Robin
authors.initials: R
authors.lastname: Haw
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Bijay
authors.initials: B
authors.lastname: Jassal
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Steven
authors.initials: S
authors.lastname: Jupe
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Florian
authors.initials: F
authors.lastname: Korninger
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Sheldon
authors.initials: S
authors.lastname: McKay
authors.affiliation: NYU School of Medicine, New York, NY 10016, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Matthews
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Bruce
authors.initials: B
authors.lastname: May
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Marija
authors.initials: M
authors.lastname: Milacic
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Karen
authors.initials: K
authors.lastname: Rothfels
authors.affiliation: NYU School of Medicine, New York, NY 10016, USA.
authors.forename: Veronica
authors.initials: V
authors.lastname: Shamovsky
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Marissa
authors.initials: M
authors.lastname: Webber
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Joel
authors.initials: J
authors.lastname: Weiser
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Williams
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.
authors.forename: Guanming
authors.initials: G
authors.lastname: Wu
authors.affiliation: Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada Lincoln.Stein@oicr.on.ca.
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK National Center for Protein Sciences, Beijing, China hhe@ebi.ac.uk.
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.affiliation: NYU School of Medicine, New York, NY 10016, USA deustp01@med.nyu.edu.
authors.forename: Peter
authors.initials: P
authors.lastname: D'Eustachio
mesh_terms: D062126:Databases, Chemical; D015870:Gene Expression; D006801:Humans; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways; D011506:Proteins / Q000378:metabolism; D015398:Signal Transduction; D012984:Software
chemical_list: D011506:Proteins