TY - JOUR
T1 - Reactome
T2 - A database of reactions, pathways and biological processes
AU - Croft, David
AU - O'Kelly, Gavin
AU - Wu, Guanming
AU - Haw, Robin
AU - Gillespie, Marc
AU - Matthews, Lisa
AU - Caudy, Michael
AU - Garapati, Phani
AU - Gopinath, Gopal
AU - Jassal, Bijay
AU - Jupe, Steven
AU - Kalatskaya, Irina
AU - MayMahajan, Shahana
AU - May, Bruce
AU - Ndegwa, Nelson
AU - Schmidt, Esther
AU - Shamovsky, Veronica
AU - Yung, Christina
AU - Birney, Ewan
AU - Hermjakob, Henning
AU - D'Eustachio, Peter
AU - Stein, Lincoln
N1 - Funding Information:
National Human Genome Research Institute at the National Institutes of Health (grant number P41 HG003751); European Union 6th Framework Programme ‘ENFIN’ (grant number LSHG-CT-2005-518254). Funding for open access charge: Ontario Institute for Cancer Research.
PY - 2011/1
Y1 - 2011/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=78651275182&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78651275182&partnerID=8YFLogxK
U2 - 10.1093/nar/gkq1018
DO - 10.1093/nar/gkq1018
M3 - Article
C2 - 21067998
AN - SCOPUS:78651275182
SN - 0305-1048
VL - 39
SP - D691-D697
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -