Discovery of cancer common and specific driver gene sets

doi:10.1093/nar/gkx089

CSpace > 应用数学研究所

	Discovery of cancer common and specific driver gene sets
	Zhang, Junhua1 ; Zhang, Shihua1,2
	2017-06-02
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	45 期号:10 页码:14
摘要	Cancer is known as a disease mainly caused by gene alterations. Discovery of mutated driver pathways or gene sets is becoming an important step to understand molecular mechanisms of carcinogenesis. However, systematically investigating commonalities and specificities of driver gene sets among multiple cancer types is still a great challenge, but this investigation will undoubtedly benefit deciphering cancers and will be helpful for personalized therapy and precision medicine in cancer treatment. In this study, we propose two optimization models to de novo discover common driver gene sets among multiple cancer types (ComMDP) and specific driver gene sets of one certain or multiple cancer types to other cancers (SpeMDP), respectively. We first apply ComMDP and SpeMDP to simulated data to validate their efficiency. Then, we further apply these methods to 12 cancer types from The Cancer Genome Atlas (TCGA) and obtain several biologically meaningful driver pathways. As examples, we construct a common cancer pathway model for BRCA and OV, infer a complex driver pathway model for BRCA carcinogenesis based on common driver gene sets of BRCA with eight cancer types, and investigate specific driver pathways of the liquid cancer lymphoblastic acutemyeloid leukemia (LAML) versus other solid cancer types. In these processes more candidate cancer genes are also found.
DOI	10.1093/nar/gkx089
语种	英语
资助项目	National Natural Science Foundation of China[61379092] ; National Natural Science Foundation of China[61422309] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[11661141019] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Outstanding Young Scientist Program of CAS ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008] ; Key Laboratory of Random Complex Structures and Data Science, CAS[2008DP173182]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000402510700011
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/25701
专题	应用数学研究所
通讯作者	Zhang, Junhua; Zhang, Shihua
作者单位	1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Junhua,Zhang, Shihua. Discovery of cancer common and specific driver gene sets[J]. NUCLEIC ACIDS RESEARCH,2017,45(10):14.
APA	Zhang, Junhua,&Zhang, Shihua.(2017).Discovery of cancer common and specific driver gene sets.NUCLEIC ACIDS RESEARCH,45(10),14.
MLA	Zhang, Junhua,et al."Discovery of cancer common and specific driver gene sets".NUCLEIC ACIDS RESEARCH 45.10(2017):14.