Reactome: a database of reactions, pathways and biological processes

被引：1199

作者：

Croft, David ^{[2
]}

O'Kelly, Gavin ^{[2
]}

Wu, Guanming ^{[1
]}

Haw, Robin ^{[1
]}

Gillespie, Marc ^{[3
]}

Matthews, Lisa ^{[4
]}

Caudy, Michael ^{[1
]}

Garapati, Phani ^{[2
]}

Gopinath, Gopal ^{[5
]}

Jassal, Bijay ^{[2
]}

Jupe, Steven ^{[2
]}

Kalatskaya, Irina ^{[1
]}

Mahajan, Shahana ^{[4
,6
]}

May, Bruce ^{[1
]}

Ndegwa, Nelson ^{[2
]}

Schmidt, Esther ^{[2
]}

Shamovsky, Veronica ^{[4
]}

Yung, Christina ^{[1
]}

Birney, Ewan ^{[2
]}

Hermjakob, Henning ^{[2
]}

D'Eustachio, Peter ^{[4
]}

Stein, Lincoln ^{[1
,7
,8
]}

机构：

[1] Ontario Inst Canc Res Informat & Biocomp, Toronto, ON M5G 0A3, Canada

[2] Wellcome Trust Genome Campus, European Bioinformat Inst, Cambridge CB10 1SD, England

[3] St Johns Univ, Coll Pharm & Allied Hlth Profess, Queens, NY 11439 USA

[4] NYU, Sch Med, Dept Biochem, New York, NY 10016 USA

[5] US FDA, Ctr Food Safety & Appl Nutr, Laurel, MD 20708 USA

[6] CUNY Hunter Coll, Sch Hlth Sci, New York, NY 10010 USA

[7] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[8] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家卫生研究院;

关键词：

COMMUNITY STANDARD; PHYLOGENETIC TREES; REPRESENTATION; COLLECTION;

D O I：

10.1093/nar/gkq1018

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D691 / D697

页数：7

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