Reactome: a knowledge base of biologic pathways and processes

被引:445
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.
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页数:13
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共 31 条
  • [21] Web-based kinetic modelling using JWS Online
    Olivier, BG
    Snoep, JL
    [J]. BIOINFORMATICS, 2004, 20 (13) : 2143 - 2144
  • [22] Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    Paley, SM
    Karp, PD
    [J]. BIOINFORMATICS, 2002, 18 (05) : 715 - 724
  • [23] Development of human protein reference database as an initial platform for approaching systems biology in humans
    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
    [J]. 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
    Ramani, AK
    Bunescu, RC
    Mooney, RJ
    Marcotte, EM
    [J]. 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
    Sartipy, P
    Loskutoff, DJ
    [J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (52) : 52298 - 52306
  • [27] Cytoscape: A software environment for integrated models of biomolecular interaction networks
    Shannon, P
    Markiel, A
    Ozier, O
    Baliga, NS
    Wang, JT
    Ramage, D
    Amin, N
    Schwikowski, B
    Ideker, T
    [J]. GENOME RESEARCH, 2003, 13 (11) : 2498 - 2504
  • [28] Na+-dependent purine nucleoside transporter from human kidney:: cloning and functional characterization
    Wang, J
    Su, SF
    Dresser, MJ
    Schaner, ME
    Washington, CB
    Giacomini, KM
    [J]. AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY, 1997, 273 (06) : F1058 - F1065
  • [29] The Universal Protein Resource (UniProt): an expanding universe of protein information
    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
    [J]. 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
    Yang, X
    Pratley, RE
    Tokraks, S
    Bogardus, C
    Permana, PA
    [J]. DIABETOLOGIA, 2002, 45 (11) : 1584 - 1593