Enabling a systems biology approach to immunology: focus on innate immunity

被引:92
作者
Gardy, Jennifer L. [1 ]
Lynn, David J. [2 ]
Brinkman, Fiona S. L. [2 ]
Hancock, Robert E. W. [1 ]
机构
[1] Univ British Columbia, Ctr Microbial Dis & Immun Res, Vancouver, BC V6T 1Z4, Canada
[2] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada
基金
美国国家卫生研究院; 加拿大健康研究院;
关键词
PROTEIN-INTERACTION NETWORKS; GENE-EXPRESSION DATA; TOLL-LIKE-RECEPTORS; MACROPHAGE ACTIVATION; CHROMATIN IMMUNOPRECIPITATION; INTERACTION DATABASE; FUNCTIONAL GENOMICS; REGULATORY NETWORKS; ADAPTIVE IMMUNITY; CYTOSCAPE PLUGIN;
D O I
10.1016/j.it.2009.03.009
中图分类号
R392 [医学免疫学]; Q939.91 [免疫学];
学科分类号
100102 ;
摘要
Immunity is not simply the product of a series of discrete linear signalling pathways; rather it is comprised of a complex set of integrated responses arising from a dynamic network of thousands of molecules subject to multiple influences. Its behaviour often cannot be explained or predicted solely by examining its components. Here, we review recently developed resources for the systems-level investigation of immunity. Although innate immunity is emphasized here, its considerable overlap with adaptive immunity makes many of these resources relevant to both arms of the immune response. We discuss recent studies implementing these approaches and illustrate the potential of systems biology to generate novel insights into the complexities of innate immunity.
引用
收藏
页码:249 / 262
页数:14
相关论文
共 107 条
[71]   A functional and regulatory map of asthma [J].
Noverstern, Noa ;
Itzhaki, Zohar ;
Manor, Ohad ;
Friedman, Nir ;
Kaminski, Naftali .
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, 2008, 38 (03) :324-336
[72]   A comprehensive map of the toll-like receptor signaling network [J].
Oda, Kanae ;
Kitano, Hiroaki .
MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0015
[73]   The minimum information required for reporting a molecular interaction experiment (MIMIx) [J].
Orchard, Sandra ;
Salwinski, Lukasz ;
Kerrien, Samuel ;
Montecchi-Palazzi, Luisa ;
Oesterheld, Matthias ;
Stuempflen, Volker ;
Ceol, Arnaud ;
Chatr-aryamontri, Andrew ;
Armstrong, John ;
Woollard, Peter ;
Salama, John J. ;
Moore, Susan ;
Wojcik, Jerome ;
Bader, Gary D. ;
Vidal, Marc ;
Cusick, Michael E. ;
Gerstein, Mark ;
Gavin, Anne-Claude ;
Superti-Furga, Giulio ;
Greenblatt, Jack ;
Bader, Joel ;
Uetz, Peter ;
Tyers, Mike ;
Legrain, Pierre ;
Fields, Stan ;
Mulder, Nicola ;
Gilson, Michael ;
Niepmann, Michael ;
Burgoon, Lyle ;
De Las Rivas, Javier ;
Prieto, Carlos ;
Perreau, Victoria M. ;
Hogue, Chris ;
Mewes, Hans-Werner ;
Apweiler, Rolf ;
Xenarios, Ioannis ;
Eisenberg, David ;
Cesareni, Gianni ;
Hermjakob, Henning .
NATURE BIOTECHNOLOGY, 2007, 25 (08) :894-898
[74]   Interaction between the HCVNS3 protein and the host TBK1 protein leads to inhibition of cellular antiviral responses [J].
Otsuka, M ;
Kato, N ;
Moriyama, M ;
Taniguchi, H ;
Wang, Y ;
Dharel, N ;
Kawabe, T ;
Omata, M .
HEPATOLOGY, 2005, 41 (05) :1004-1012
[75]   ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression [J].
Parkinson, Helen ;
Kapushesky, Misha ;
Kolesnikov, Nikolay ;
Rustici, Gabriella ;
Shojatalab, Mohammad ;
Abeygunawardena, Niran ;
Berube, Hugo ;
Dylag, Miroslaw ;
Emam, Ibrahim ;
Farne, Anna ;
Holloway, Ele ;
Lukk, Margus ;
Malone, James ;
Mani, Roby ;
Pilicheva, Ekaterina ;
Rayner, Tim F. ;
Rezwan, Faisal ;
Sharma, Anjan ;
Williams, Eleanor ;
Bradley, Xiangqun Zheng ;
Adamusiak, Tomasz ;
Brandizi, Marco ;
Burdett, Tony ;
Coulson, Richard ;
Krestyaninova, Maria ;
Kurnosov, Pavel ;
Maguire, Eamonn ;
Neogi, Sudeshna Guha ;
Rocca-Serra, Philippe ;
Sansone, Susanna-Assunta ;
Sklyar, Nataliya ;
Zhao, Mengyao ;
Sarkans, Ugis ;
Brazma, Alvis .
NUCLEIC ACIDS RESEARCH, 2009, 37 :D868-D872
[76]   MicroRNAs in the immune response [J].
Pedersen, Irene ;
David, Michael .
CYTOKINE, 2008, 43 (03) :391-394
[77]   Identification of a Common Gene Expression Response in Different Lung Inflammatory Diseases in Rodents and Macaques [J].
Pennings, Jeroen L. A. ;
Kimman, Tjeerd G. ;
Janssen, Riny .
PLOS ONE, 2008, 3 (07)
[78]   Proteome-scale analysis of biochemical activity [J].
Phizicky, Eric M. ;
Grayhack, Elizabeth J. .
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 2006, 41 (05) :315-327
[79]   Network modeling links breast cancer susceptibility and centrosome dysfunction [J].
Pujana, Miguel Angel ;
Han, Jing-Dong J. ;
Starita, Lea M. ;
Stevens, Kristen N. ;
Tewari, Muneesh ;
Ahn, Jin Sook ;
Rennert, Gad ;
Moreno, Victor ;
Kirchhoff, Tomas ;
Gold, Bert ;
Assmann, Volker ;
ElShamy, Wael M. ;
Rual, Jean-Francois ;
Levine, Douglas ;
Rozek, Laura S. ;
Gelman, Rebecca S. ;
Gunsalus, Kristin C. ;
Greenberg, Roger A. ;
Sobhian, Bijan ;
Bertin, Nicolas ;
Venkatesan, Kavitha ;
Ayivi-Guedehoussou, Nono ;
Sole, Xavier ;
Hernandez, Pilar ;
Lazaro, Conxi ;
Nathanson, Katherine L. ;
Weber, Barbara L. ;
Cusick, Michael E. ;
Hill, David E. ;
Offit, Kenneth ;
Livingston, David M. ;
Gruber, Stephen B. ;
Parvin, Jeffrey D. ;
Vidal, Marc .
NATURE GENETICS, 2007, 39 (11) :1338-1349
[80]   A map of human protein interactions derived from co-expression of human mRNAs and their orthologs [J].
Ramani, Arun K. ;
Li, Zhihua ;
Hart, G. Traver ;
Carlson, Mark W. ;
Boutz, Daniel R. ;
Marcotte, Edward M. .
MOLECULAR SYSTEMS BIOLOGY, 2008, 4 (1)