Reactome: a knowledge base of biologic pathways and processes

被引：448

作者：

Vastrik, Imre

D'Eustachio, Peter

Schmidt, Esther

Joshi-Tope, Geeta

Gopinath, Gopal

Croft, David

de Bono, Bernard

Gillespie, Marc

Jassal, Bijay

Lewis, Suzanna

Matthews, Lisa

Wu, Guanming

Birney, Ewan

Stein, Lincoln

机构：

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

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

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

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

[5] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA

来源：

GENOME BIOLOGY | 2007年 / 8卷 / 03期

关键词：

INSULIN-RESISTANT; SYSTEMS BIOLOGY; PROTEIN; DATABASE; NETWORK; GENES; MODELS; BIND; TOOL;

D O I：

10.1186/gb-2007-8-3-r39

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Reactome http://www.reactome.org, an online curated resource for human pathway data, provides infrastructure for computation across the biologic reaction network. We use Reactome to infer equivalent reactions in multiple nonhuman species, and present data on the reliability of these inferred reactions for the distantly related eukaryote Saccharomyces cerevisiae. Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets.

引用

页数：13

共 31 条

[21] Web-based kinetic modelling using JWS Online [J].

Olivier, BG ;

Snoep, JL .

BIOINFORMATICS, 2004, 20 (13) :2143-2144

[22] Evaluation of computational metabolic-pathway predictions for Helicobacter pylori [J].

Paley, SM ;

Karp, PD .

BIOINFORMATICS, 2002, 18 (05) :715-724

[23] Development of human protein reference database as an initial platform for approaching systems biology in humans [J].

Peri, S ;

Navarro, JD ;

Amanchy, R ;

Kristiansen, TZ ;

Jonnalagadda, CK ;

Surendranath, V ;

Niranjan, V ;

Muthusamy, B ;

Gandhi, TKB ;

Gronborg, M ;

Ibarrola, N ;

Deshpande, N ;

Shanker, K ;

Shivashankar, HN ;

Rashmi, BP ;

Ramya, MA ;

Zhao, ZX ;

Chandrika, KN ;

Padma, N ;

Harsha, HC ;

Yatish, AJ ;

Kavitha, MP ;

Menezes, M ;

Choudhury, DR ;

Suresh, S ;

Ghosh, N ;

Saravana, R ;

Chandran, S ;

Krishna, S ;

Joy, M ;

Anand, SK ;

Madavan, V ;

Joseph, A ;

Wong, GW ;

Schiemann, WP ;

Constantinescu, SN ;

Huang, LL ;

Khosravi-Far, R ;

Steen, H ;

Tewari, M ;

Ghaffari, S ;

Blobe, GC ;

Dang, CV ;

Garcia, JGN ;

Pevsner, J ;

Jensen, ON ;

Roepstorff, P ;

Deshpande, KS ;

Chinnaiyan, AM ;

Hamosh, A .

GENOME RESEARCH, 2003, 13 (10) :2363-2371

[24] Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome [J].

Ramani, AK ;

Bunescu, RC ;

Mooney, RJ ;

Marcotte, EM .

GENOME BIOLOGY, 2005, 6 (05)

[25]

Romero P, 2005, GENOME BIOL, V6

[26] Expression profiling identifies genes that continue to respond to insulin in adipocytes made insulin-resistant by treatment with tumor necrosis factor-α [J].

Sartipy, P ;

Loskutoff, DJ .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (52) :52298-52306

[27] Cytoscape: A software environment for integrated models of biomolecular interaction networks [J].

Shannon, P ;

Markiel, A ;

Ozier, O ;

Baliga, NS ;

Wang, JT ;

Ramage, D ;

Amin, N ;

Schwikowski, B ;

Ideker, T .

GENOME RESEARCH, 2003, 13 (11) :2498-2504

[28] Na+-dependent purine nucleoside transporter from human kidney:: cloning and functional characterization [J].

Wang, J ;

Su, SF ;

Dresser, MJ ;

Schaner, ME ;

Washington, CB ;

Giacomini, KM .

AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY, 1997, 273 (06) :F1058-F1065

[29] The Universal Protein Resource (UniProt): an expanding universe of protein information [J].

Wu, Cathy H. ;

Apweiler, Rolf ;

Bairoch, Amos ;

Natale, Darren A. ;

Barker, Winona C. ;

Boeckmann, Brigitte ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Huang, Hongzhan ;

Lopez, Rodrigo ;

Magrane, Michele ;

Martin, Maria J. ;

Mazumder, Raja ;

O'Donovan, Claire ;

Redaschi, Nicole ;

Suzek, Baris .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D187-D191

[30] Microarray profiling of skeletal muscle tissues from equally obese, non-diabetic insulin-sensitive and insulin-resistant Pima Indians [J].

Yang, X ;

Pratley, RE ;

Tokraks, S ;

Bogardus, C ;

Permana, PA .

DIABETOLOGIA, 2002, 45 (11) :1584-1593

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