DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
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DOI：
10.1186/gb-2012-13-12-r124
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发表时间：
2012-12-22
期刊：
影响因子：
12.3
通讯作者：
Shah SP
中科院分区：
文献类型：
--
作者：
Bashashati A;Haffari G;Ding J;Ha G;Lui K;Rosner J;Huntsman DG;Caldas C;Aparicio SA;Shah SP
对肿瘤基因组和转录本的同时询问正在史无前例的全球努力中进行。然而，尽管有必要将调控基因表达网络的驱动突变与转录惰性的乘客突变分开，但确定单个突变对转录网络的影响的强大计算方法还不成熟。我们引入了一个新的计算框架，DriverNet，通过它们对mRNA表达网络的影响来识别可能的驱动突变。对四个癌症数据集的应用表明，与转录网络中断相关的罕见候选驱动程序突变的流行，以及由相邻致癌驱动因素和代谢驱动因素的拷贝数共修饰引起的致癌和代谢网络的同时调节。DriverNet可在BioConductor或http://compbio.bccrc.ca/software/drivernet/.上获得
Simultaneous interrogation of tumor genomes and transcriptomes is underway in unprecedented global efforts. Yet, despite the essential need to separate driver mutations modulating gene expression networks from transcriptionally inert passenger mutations, robust computational methods to ascertain the impact of individual mutations on transcriptional networks are underdeveloped. We introduce a novel computational framework, DriverNet, to identify likely driver mutations by virtue of their effect on mRNA expression networks. Application to four cancer datasets reveals the prevalence of rare candidate driver mutations associated with disrupted transcriptional networks and a simultaneous modulation of oncogenic and metabolic networks, induced by copy number co-modification of adjacent oncogenic and metabolic drivers. DriverNet is available on Bioconductor or at http://compbio.bccrc.ca/software/drivernet/.
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影响因子：
9.9
作者：
Nelander, Sven;Wang, Weiqing;Nilsson, Bjoern;She, Qing-Bai;Pratilas, Christine;Rosen, Neal;Gennemark, Peter;Sander, Chris
通讯作者：
Sander, Chris
DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
--
影响因子：
11.1
作者：
Holland, Daniel G.;Burleigh, Angela;Git, Anna;Goldgraben, Mae A.;Perez-Mancera, Pedro A.;Chin, Suet-Feung;Hurtado, Antonio;Bruna, Alejandro;Ali, H. Raza;Greenwood, Wendy;Dunning, Mark J.;Samarajiwa, Shamith;Menon, Suraj;Rueda, Oscar M.;Lynch, Andy G.;McKinney, Steven;Ellis, Ian O.;Eaves, Connie J.;Carroll, Jason S.;Curtis, Christina;Aparicio, Samuel;Caldas, Carlos
通讯作者：
Caldas, Carlos
影响因子：
64.8
作者：
Curtis, Christina;Shah, Sohrab P.;Chin, Suet-Feung;Turashvili, Gulisa;Rueda, Oscar M.;Dunning, Mark J.;Speed, Doug;Lynch, Andy G.;Samarajiwa, Shamith;Yuan, Yinyin;Graef, Stefan;Ha, Gavin;Haffari, Gholamreza;Bashashati, Ali;Russell, Roslin;McKinney, Steven;Langerod, Anita;Green, Andrew;Provenzano, Elena;Wishart, Gordon;Pinder, Sarah;Watson, Peter;Markowetz, Florian;Murphy, Leigh;Ellis, Ian;Purushotham, Arnie;Borresen-Dale, Anne-Lise;Brenton, James D.;Tavare, Simon;Caldas, Carlos;Aparicio, Samuel
通讯作者：
Aparicio, Samuel
DOI：
10.1126/science.1164382
发表时间：
2008-09-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Parsons DW;Jones S;Zhang X;Lin JC;Leary RJ;Angenendt P;Mankoo P;Carter H;Siu IM;Gallia GL;Olivi A;McLendon R;Rasheed BA;Keir S;Nikolskaya T;Nikolsky Y;Busam DA;Tekleab H;Diaz LA Jr;Hartigan J;Smith DR;Strausberg RL;Marie SK;Shinjo SM;Yan H;Riggins GJ;Bigner DD;Karchin R;Papadopoulos N;Parmigiani G;Vogelstein B;Velculescu VE;Kinzler KW
通讯作者：
Kinzler KW