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., Kataskaya, I., Mahajan, S., May, B., Ndegwa, N., Schmidt, E., Shamovsky, V., Yung, C., Birney, E., Hermjakob, H., D'Eustachio, P., Stein, L. D. (January 2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 39 (Suppl ). D691-7. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

[thumbnail of Paper]
Preview
PDF (Paper)
Stein Nucleic Acid Res 2011.pdf - Published Version

Download (11MB) | Preview
URL: https://www.ncbi.nlm.nih.gov/pubmed/21067998
DOI: 10.1093/nar/gkq1018

Abstract

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > analysis and processing > NETBAG
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date: 9 January 2011
Date Deposited: 28 Sep 2011 14:08
Last Modified: 08 Nov 2017 15:23
PMCID: PMC3013646
Related URLs:
URI: https://repository.cshl.edu/id/eprint/15396

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving