Pathway Commons, a web resource for biological pathway data

By Ethan G. Cerami, Benjamin E. Gross, Emek Demir, I. Rodchenkov, O. Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Christopher Sander. Nucleic Acids Res., 2010

1,141 citations recorded by the source corpus.

Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687 000 interactions and will be continually expanded and updated.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/79bd9c6963c7ed09235b444a6a85074437e44cc9

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Citations in the corpus

Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome (2017, methodology): “The construction of the PPI network itself is described in detail elsewhere 11 , and is obtained by integrating various interaction databases which form part of Pathway Commons (www.pathwaycommons.org) 48 .”
Systematic integration of biomedical knowledge prioritizes drugs for repurposing (2017, methodology): “…; MacArthur et al., 2017 ; Himmelstein, 2015h ; Himmelstein et al., 2015v ) Reactome PW, GpPW custom 2 OD RRID:SCR_003485 ( Fabregat et al., 2016 ; Cerami et al., 2011 ; Pico and Himmelstein, 2015 ; Himmelstein and Pico, 2016a ) LINCS L1000 CdG, CuG, Gr > G custom 2 OD ( Himmelstein and Chung,…”
Inferring causal molecular networks: empirical assessment through a community-based effort (2016, methodology): “The matrices were obtained via simulated heat diffusion applied to links derived from the Pathway Commons database 35 .”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “Finally, the PANTHER pathway is in the process of being integrated into Pathway Commons 23 .”
TSGene: a web resource for tumor suppressor genes (2012, methodology): “To view the interaction partners, users can click on ‘Interaction’ to expand different interaction categories, including physical interactions from high-throughput experiments, metabolic and signaling interactions from known pathway databases (41).”
The BioGRID interaction database: 2015 update (2014, background): “…also accessible to the individual researcher indirectly through a number of other biological databases including NCBI Entrez-Gene (48), Uniprot (49), DroID (80), GermOnline (81), FlyBase (42), TAIR (73), SGD (41), PomBase (43), STRING (47), iRefIndex (82), GeneMania (83) and Pathway Commons (50).”
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas (2019, background): “Pathway Commons, a web resource for biological pathway data.”
Mutual exclusivity analysis identifies oncogenic network modules. (2012, methodology): “Pathway data sets for Reactome (Release 35, Dec 2010), NCI/Nature Pathway Interaction Database (Sept 2010 Release), and the MSKCC Cancer Cell Map (May 2006 Release) were downloaded in the Simple Interaction Format (SIF) from Pathway Commons (Cerami et al. 2011) on April 4, 2011.”
Network-based stratification of tumor mutations (2013, methodology): “PathwayCommons aggregates interactions from several pathway and interaction databases, focused primarily on physical protein-protein interactions (PPIs) and functional relationships between genes in canonical regulatory, signaling and metabolic pathways (including hallmark pathways of cancer).”
WikiPathways: building research communities on biological pathways (2011, methodology): “This for example allows integration of the content into pathway unification efforts such as Pathway Commons (16).”
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 (2013, background): “Most of these tools integrate multiple centrally curated functional databases, such as Gene Ontology (GO) (5), KEGG (6), Pathway Commons (7) and MSigDB (8).”