The Reactome pathway Knowledgebase

被引：621

作者：

Fabregat, Antonio ^{[1
]}

Sidiropoulos, Konstantinos ^{[1
]}

Garapati, Phani ^{[1
]}

Gillespie, Marc ^{[2
,3
]}

Hausmann, Kerstin ^{[1
]}

Haw, Robin ^{[2
]}

Jassal, Bijay ^{[2
]}

Jupe, Steven ^{[1
]}

Korninger, Florian ^{[1
]}

McKay, Sheldon ^{[2
]}

Matthews, Lisa ^{[4
]}

May, Bruce ^{[2
]}

Milacic, Marija ^{[2
]}

Rothfels, Karen ^{[2
]}

Shamovsky, Veronica ^{[4
]}

Webber, Marissa ^{[2
]}

Weiser, Joel ^{[2
]}

Williams, Mark ^{[1
]}

Wu, Guanming ^{[2
]}

Stein, Lincoln ^{[2
,5
,6
]}

Hermjakob, Henning ^{[1
,7
]}

D'Eustachio, Peter ^{[4
]}

机构：

[1] European Mol Biol Lab, European Bioinformat Inst EMBL EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[2] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

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

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

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

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

[7] Natl Ctr Prot Sci, Beijing, Peoples R China

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkv1351

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：

The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.

引用

页码：D481 / D487

页数：7

共 5 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2]

Croft D, 2014, NUCLEIC ACIDS RES, V42, pD472, DOI [10.1093/nar/gkt1102, 10.1093/nar/gkz1031]

[3]

Gene Ontology Consortium, 2015, NUCLEIC ACIDS RES, V43, pD1049

[4] Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data [J].

Kibbe, Warren A. ;

Arze, Cesar ;

Felix, Victor ;

Mitraka, Elvira ;

Bolton, Evan ;

Fu, Gang ;

Mungall, Christopher J. ;

Binder, Janos X. ;

Malone, James ;

Vasant, Drashtti ;

Parkinson, Helen ;

Schriml, Lynn M. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D1071-D1078

[5] High Precision Platelet Releasate Definition by Quantitative Reversed Protein Profiling-Brief Report [J].

Wijten, Patrick ;

van Holten, Thijs ;

Woo, Liy Liy ;

Bleijerveld, Onno B. ;

Roest, Mark ;

Heck, Albert J. R. ;

Scholten, Arjen .

ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 2013, 33 (07) :1635-1638

← 1 →