Arabidopsis reactome: A foundation knowledgebase for plant systems biology

被引：41

作者：

Tsesmetzis, Nicolas ^{[1
]}

Couchman, Matthew ^{[1
]}

Higgins, Janet ^{[1
]}

Smith, Alison ^{[2
]}

Doonan, John H. ^{[3
]}

Seifert, Georg J. ^{[3
]}

Schmidt, Esther E. ^{[4
]}

Vastrik, Imre ^{[4
]}

Birney, Ewan ^{[4
]}

Wu, Guanming ^{[5
]}

D'Eustachio, Peter ^{[5
,6
]}

Stein, Lincoln D. ^{[5
]}

Morris, Richard J. ^{[1
]}

Bevan, Michael W. ^{[3
]}

Walsh, Sean V. ^{[1
]}

机构：

[1] John Innes Inst, Dept Computat & Syst Biol, Norwich NR4 7UH, Norfolk, England

[2] John Innes Inst, Dept Metab Biol, Norwich NR4 7UH, Norfolk, England

[3] John Innes Inst, Dept Cell & Dev Biol, Norwich NR4 7UH, Norfolk, England

[4] European Bioinformat Inst, Cambridge CB10 1SD, England

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

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

来源：

PLANT CELL | 2008年 / 20卷 / 06期

基金：

英国生物技术与生命科学研究理事会;

关键词：

D O I：

10.1105/tpc.108.057976

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：

New ways of capturing and representing biological knowledge are needed to enable individual researchers to remain abreast of relevant discoveries and to permit computational approaches for interpreting the large volumes of diverse data generated by modern biological research. Here, we describe a promising approach that expands the term "reaction'' to represent biological processes. We show how users can represent a wide variety of biological processes in plants in terms of the concept of a reaction and assemble the information obtained from the model plant Arabidopsis thaliana into an online knowledgebase called Arabidopsis Reactome. Its curated and imported pathways currently cover similar to 8% of the Arabidopsis proteome. Arabidopsis Reactome events have also been electronically projected onto five other predicted plant proteomes. Such a system allows the visualization and interpretation of high-throughput data, hypothesis formulation in systems biology, and is a useful learning resource. The Arabidopsis Reactome project (www.arabidopsisreactome.org) is open access, open source, and open to contributions.

引用

页码：1426 / 1436

页数：11

共 55 条

[1] Moving forward in reverse:: genetic technologies to enable genome-wide phenomic screens in Arabidopsis [J].

Alonso, Jose M. ;

Ecker, Joseph R. .

NATURE REVIEWS GENETICS, 2006, 7 (07) :524-536

[2]

[Anonymous], 1968, An introduction to probability theory and its applications

[3] 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

[4] An automated method for finding molecular complexes in large protein interaction networks [J].

Bader, GD ;

Hogue, CW .

BMC BIOINFORMATICS, 2003, 4 (1)

[5] How to infer gene networks from expression profiles [J].

Bansal, Mukesh ;

Belcastro, Vincenzo ;

Ambesi-Impiombato, Alberto ;

di Bernardo, Diego .

MOLECULAR SYSTEMS BIOLOGY, 2007, 3 (1)

[6] Less is more in modeling large genetic networks [J].

Bornholdt, S .

SCIENCE, 2005, 310 (5747) :449-+

[7] Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana [J].

Clark, Richard M. ;

Schweikert, Gabriele ;

Toomajian, Christopher ;

Ossowski, Stephan ;

Zeller, Georg ;

Shinn, Paul ;

Warthmann, Norman ;

Hu, Tina T. ;

Fu, Glenn ;

Hinds, David A. ;

Chen, Huaming ;

Frazer, Kelly A. ;

Huson, Daniel H. ;

Schoelkopf, Bernhard ;

Nordborg, Magnus ;

Raetsch, Gunnar ;

Ecker, Joseph R. ;

Weigel, Detlef .

SCIENCE, 2007, 317 (5836) :338-342

[8] NASCArrays: a repository for microarray data generated by NASC's transcriptomics service [J].

Craigon, DJ ;

James, N ;

Okyere, J ;

Higgins, J ;

Jotham, J ;

May, S .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D575-D577

[9] AtPID:: Arabidopsis thaliana protein interactome database -: an integrative platform for plant systems biology [J].

Cui, Jian ;

Li, Peng ;

Li, Guang ;

Xu, Feng ;

Zhao, Chen ;

Li, Yuhua ;

Yang, Zhongnan ;

Wang, Guang ;

Yu, Qingbo ;

Li, Yixue ;

Shi, Tieliu .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D999-D1008

[10] Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast [J].

Davidich, Maria I. ;

Bornholdt, Stefan .

PLOS ONE, 2008, 3 (02)

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