Reactome pathway analysis to enrich biological discovery in proteomics data sets

Haw, R., Hermjakob, H., D'Eustachio, P., Stein, L. D. (2011) Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics, 11 (18). pp. 3598-3613. ISSN 16159853 (ISSN)

URL: https://www.ncbi.nlm.nih.gov/pubmed/21751369
DOI: 10.1002/pmic.201100066

Abstract

Reactome (http://www.reactome.org) is an open-source, expert-authored, peer-reviewed, manually curated database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Pathway Browser is a Systems Biology Graphical Notation-like visualization system that supports manual navigation of pathways by zooming, scrolling and event highlighting, and that exploits PSI Common Query Interface web services to overlay pathways with molecular interaction data from the Reactome Functional Interaction Network and interaction databases such as IntAct, ChEMBL and BioGRID. Pathway and expression analysis tools employ web services to provide ID mapping, pathway assignment and over-representation analysis of user-supplied data sets. By applying Ensembl Compara to curated human proteins and reactions, Reactome generates pathway inferences for 20 other species. The Species Comparison tool provides a summary of results for each of these species as a table showing numbers of orthologous proteins found by pathway from which users can navigate to inferred details for specific proteins and reactions. Reactome's diverse pathway knowledge and suite of data analysis tools provide a platform for data mining, modeling and analysis of large-scale proteomics data sets. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 8). © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Item Type: Paper
Uncontrolled Keywords: Bioinformatics BioMart Data integration Pathway analysis Pathway database Pathway visualization Tutorial
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > design
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date Deposited: 09 Nov 2011 19:10
Last Modified: 28 Feb 2018 14:14
PMCID: PMC4617659
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15643

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