Reactome: a database of reactions, pathways and biological processes.
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.
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
David
D
Croft
Gavin
G
O'Kelly
Guanming
G
Wu
Robin
R
Haw
Marc
M
Gillespie
Lisa
L
Matthews
Michael
M
Caudy
Phani
P
Garapati
Gopal
G
Gopinath
Bijay
B
Jassal
Steven
S
Jupe
Irina
I
Kalatskaya
Shahana
S
Mahajan
Bruce
B
May
Nelson
N
Ndegwa
Esther
E
Schmidt
Veronica
V
Shamovsky
Christina
C
Yung
Ewan
E
Birney
Henning
H
Hermjakob
Peter
P
D'Eustachio
Lincoln
L
Stein
D001686:Biological Phenomena; D003196:Computer Graphics; D016208:Databases, Factual; D030541:Databases, Genetic; D030562:Databases, Protein; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015398:Signal Transduction