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Cited by 117Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and ApplicationsBiomedical Text Mining and Ontologies

Reactome pathway analysis to enrich biological discovery in proteomics data sets

Open access
Haw, Robin, Hermjakob, Henning, D'Eustachio, Peter, Stein, Lincoln·2011·PROTEOMICS
DOI 10.1002/pmic.201100066PMC PMC4617659
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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).

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Authors
Haw, R., Hermjakob, H., D'Eustachio, P., & Stein, L.
Affiliations
  • Ontario Institute for Cancer Research (CA)
  • European Bioinformatics Institute (GB)
Corresponding author
Stein, Lincoln
ORCID
Venue
PROTEOMICS
Publisher
Wiley
Published
2011-09
Volume
11
Issue
18
Pages
3598-3613
ISSN
  • 1615-9853 (ISSN-L)
  • 1615-9861
DOI
10.1002/pmic.201100066
PMC
PMC4617659
OpenAlex
W2005086972
Cited by
117
References
90
Citations by year
2026: 5 · 2025: 8 · 2024: 5 · 2023: 2 · 2022: 8 · 2021: 5 · 2020: 7 · 2019: 8 · 2018: 6 · 2017: 8 · 2016: 6 · 2015: 8 · 2014: 9 · 2013: 11 · 2012: 16
FWCI
5.33
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor, 5 d)
Locations
  • PROTEOMICS (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
Funders
  • National Human Genome Research Institute at the National Institutes of Health (P41 HG0037510)
  • European Union 6th Framework Programme ‘ENFIN’ (LSHG-CT-2005-518254)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
Reactome, pathway analysis, pathway enrichment, proteomics data analysis, pathway inference, orthologous proteins, species comparison, over-representation analysis, web services
MeSH terms
Animals, Biological Phenomena, Computer Graphics, Humans, User-Computer Interface, Signal Transduction, Internet, Databases, Protein, Proteomics, Systems Biology, Knowledge Bases, Metabolic Networks and Pathways

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