Principles and Strategies for Developing Network Models in Cancer

被引：130
作者：
Pe'er, Dana [1 ,2 ]
Hacohen, Nir [3 ,4 ,5 ]
机构：
[1] Columbia Univ, Dept Biol Sci, New York, NY 10027 USA
[2] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA
[3] Broad Inst MIT & Harvard, Cambridge Ctr 7, Cambridge, MA 02142 USA
[4] Massachusetts Gen Hosp, Ctr Immunol & Inflammatory Dis, Charlestown, MA 02129 USA
[5] Harvard Univ, Sch Med, Dept Med, Boston, MA 02115 USA
来源：
CELL | 2011年 / 144卷 / 06期
关键词：
TRANSCRIPTIONAL NETWORK; IDENTIFICATION; INHIBITION; GENE; MAP; ACTIVATION; REGULATORS; DYNAMICS; GENOME; MODULE;
D O I：
10.1016/j.cell.2011.03.001
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 flood of genome-wide data generated by high-throughput technologies currently provides biologists with an unprecedented opportunity: to manipulate, query, and reconstruct functional molecular networks of cells. Here, we outline three underlying principles and six strategies to infer network models from genomic data. Then, using cancer as an example, we describe experimental and computational approaches to infer "differential" networks that can identify genes and processes driving disease phenotypes. In conclusion, we discuss how a network-level understanding of cancer can be used to predict drug response and guide therapeutics.
引用
收藏
页码：864 / 873
页数：10
相关论文
共 48 条
  • [1] An Integrated Approach to Uncover Drivers of Cancer
    Akavia, Uri David
    Litvin, Oren
    Kim, Jessica
    Sanchez-Garcia, Felix
    Kotliar, Dylan
    Causton, Helen C.
    Pochanard, Panisa
    Mozes, Eyal
    Garraway, Levi A.
    Pe'er, Dana
    [J]. CELL, 2010, 143 (06) : 1005 - 1017
  • [2] A module of negative feedback regulators defines growth factor signaling
    Amit, Ido
    Citri, Ami
    Shay, Tal
    Lu, Yiling
    Katz, Menachem
    Zhang, Fan
    Tarcic, Gabi
    Siwak, Doris
    Lahad, John
    Jacob-Hirsch, Jasmine
    Amariglio, Ninette
    Vaisman, Nora
    Segal, Eran
    Rechavi, Gideon
    Alon, Uri
    Mills, Gordon B.
    Domany, Eytan
    Yarden, Yosef
    [J]. NATURE GENETICS, 2007, 39 (04) : 503 - 512
  • [3] Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
    Amit, Ido
    Garber, Manuel
    Chevrier, Nicolas
    Leite, Ana Paula
    Donner, Yoni
    Eisenhaure, Thomas
    Guttman, Mitchell
    Grenier, Jennifer K.
    Li, Weibo
    Zuk, Or
    Schubert, Lisa A.
    Birditt, Brian
    Shay, Tal
    Goren, Alon
    Zhang, Xiaolan
    Smith, Zachary
    Deering, Raquel
    McDonald, Rebecca C.
    Cabili, Moran
    Bernstein, Bradley E.
    Rinn, John L.
    Meissner, Alex
    Root, David E.
    Hacohen, Nir
    Regev, Aviv
    [J]. SCIENCE, 2009, 326 (5950) : 257 - 263
  • [4] A human MAP kinase interactome
    Bandyopadhyay, Sourav
    Chiang, Chih-yuan
    Srivastava, Jyoti
    Gersten, Merril
    White, Suhaila
    Bell, Russell
    Kurschner, Cornelia
    Martin, Christopher H.
    Smoot, Mike
    Sahasrabudhe, Sudhir
    Barber, Diane L.
    Chanda, Sumit K.
    Ideker, Trey
    [J]. NATURE METHODS, 2010, 7 (10) : 801 - U50
  • [5] Reverse engineering of regulatory networks in human B cells
    Basso, K
    Margolin, AA
    Stolovitzky, G
    Klein, U
    Dalla-Favera, R
    Califano, A
    [J]. NATURE GENETICS, 2005, 37 (04) : 382 - 390
  • [6] The landscape of somatic copy-number alteration across human cancers
    Beroukhim, Rameen
    Mermel, Craig H.
    Porter, Dale
    Wei, Guo
    Raychaudhuri, Soumya
    Donovan, Jerry
    Barretina, Jordi
    Boehm, Jesse S.
    Dobson, Jennifer
    Urashima, Mitsuyoshi
    Mc Henry, Kevin T.
    Pinchback, Reid M.
    Ligon, Azra H.
    Cho, Yoon-Jae
    Haery, Leila
    Greulich, Heidi
    Reich, Michael
    Winckler, Wendy
    Lawrence, Michael S.
    Weir, Barbara A.
    Tanaka, Kumiko E.
    Chiang, Derek Y.
    Bass, Adam J.
    Loo, Alice
    Hoffman, Carter
    Prensner, John
    Liefeld, Ted
    Gao, Qing
    Yecies, Derek
    Signoretti, Sabina
    Maher, Elizabeth
    Kaye, Frederic J.
    Sasaki, Hidefumi
    Tepper, Joel E.
    Fletcher, Jonathan A.
    Tabernero, Josep
    Baselga, Jose
    Tsao, Ming-Sound
    Demichelis, Francesca
    Rubin, Mark A.
    Janne, Pasi A.
    Daly, Mark J.
    Nucera, Carmelo
    Levine, Ross L.
    Ebert, Benjamin L.
    Gabriel, Stacey
    Rustgi, Anil K.
    Antonescu, Cristina R.
    Ladanyi, Marc
    Letai, Anthony
    [J]. NATURE, 2010, 463 (7283) : 899 - 905
  • [7] Integrative genomic approaches identify IKBKE as a breast cancer oncogene
    Boehm, Jesse S.
    Zhao, Jean J.
    Yao, Jun
    Kim, So Young
    Firestein, Ron
    Dunn, Ian F.
    Sjostrom, Sarah K.
    Garraway, Levi A.
    Weremowicz, Stanislawa
    Richardson, Andrea L.
    Greulich, Heidi
    Stewart, Carly J.
    Mulvey, Laura A.
    Shen, Rhine R.
    Ambrogio, Lauren
    Hirozane-Kishikawa, Tomoko
    Hill, David E.
    Vidal, Marc
    Meyerson, Matthew
    Grenier, Jennifer K.
    Hinkle, Greg
    Root, David E.
    Roberts, Thomas M.
    Lander, Eric S.
    Polyak, Kornelia
    Hahn, William C.
    [J]. CELL, 2007, 129 (06) : 1065 - 1079
  • [8] A predictive model for transcriptional control of physiology in a free living cell
    Bonneau, Richard
    Facciotti, Marc T.
    Reiss, David J.
    Schmid, Amy K.
    Pan, Min
    Kaur, Amardeep
    Thorsson, Vesteinn
    Shannon, Paul
    Johnson, Michael H.
    Bare, J. Christopher
    Longabaugh, William
    Vuthoori, Madhavi
    Whitehead, Kenia
    Madar, Aviv
    Suzuki, Lena
    Mori, Tetsuya
    Chang, Dong-Eun
    DiRuggiero, Jocelyne
    Johnson, Carl H.
    Hood, Leroy
    Baliga, Nitin S.
    [J]. CELL, 2007, 131 (07) : 1354 - 1365
  • [9] Genes that mediate breast cancer metastasis to the brain
    Bos, Paula D.
    Zhang, Xiang H. -F.
    Nadal, Cristina
    Shu, Weiping
    Gomis, Roger R.
    Nguyen, Don X.
    Minn, Andy J.
    van de Vijver, Marc J.
    Gerald, William L.
    Foekens, John A.
    Massague, Joan
    [J]. NATURE, 2009, 459 (7249) : 1005 - U137
  • [10] Carracedo A, 2008, J CLIN INVEST, V118, P3065, DOI [10.1172/JCI34739, 10.1172/jCI34739]
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