Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples

doi:10.1002/advs.201801384

	Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples
	Gao, Bo 1,2; Zhao, Yue 3,4; Li, Yang 1,2; Liu, Juntao 1; Wang, Lushan 2; Li, Guojun 1,2; Su, Zhengchang 5
刊名	ADVANCED SCIENCE
	2019-02-20
卷号	6 期号:4 页码:9
关键词	cancer genomics coverage driver modules exclusivity signaling networks
ISSN号	2198-3844
DOI	10.1002/advs.201801384
英文摘要	Mutual exclusivity of cancer driving mutations is a frequently observed phenomenon in the mutational landscape of cancer. The long tail of rare mutations complicates the discovery of mutually exclusive driver modules. The existing methods usually suffer from the problem that only few genes in some identified modules cover most of the cancer samples. To overcome this hurdle, an efficient method UniCovEx is presented via identifying mutually exclusive driver modules of balanced exclusive coverages. UniCovEx first searches for candidate driver modules with a strong topological relationship in signaling networks using a greedy strategy. It then evaluates the candidate modules by considering their coverage, exclusivity, and balance of coverage, using a novel metric termed exclusive entropy of modules, which measures how balanced the modules are. Finally, UniCovEx predicts sample-specific driver modules by solving a minimum set cover problem using a greedy strategy. When tested on 12 The Cancer Genome Atlas datasets of different cancer types, UniCovEx shows a significant superiority over the previous methods. The software is available at: https://sourcefoge.net/projects/cancer-pathway/files/.
资助项目	National Natural Science Foundation of China[61432010] ; National Natural Science Foundation of China[61771009] ; National Key Research and Development Program of China[2016YFB0201702] ; US National Science Foundation[DBI-1661332] ; NIH[R01GM106013] ; program for outstanding PhD candidate of Shandong University
WOS研究方向	Chemistry ; Science & Technology - Other Topics ; Materials Science
语种	英语
出版者	WILEY
WOS记录号	WOS:000459168700003
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/32597]
专题	中国科学院数学与系统科学研究院
通讯作者	Li, Guojun; Su, Zhengchang
作者单位	1.Shandong Univ, Sch Math, Jinan 250100, Shandong, Peoples R China 2.Shandong Univ, State Key Lab Microbial Technol, Jinan 250100, Shandong, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, IAM, MADIS,NCMIS, Beijing 100190, Peoples R China 4.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 5.Univ North Carolina Charlotte, Coll Comp & Informat, Dept Bioinformat & Genom, 9201 Univ City Blvd, Charlotte, NC 28223 USA
推荐引用方式 GB/T 7714	Gao, Bo,Zhao, Yue,Li, Yang,et al. Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples[J]. ADVANCED SCIENCE,2019,6(4):9.
APA	Gao, Bo.,Zhao, Yue.,Li, Yang.,Liu, Juntao.,Wang, Lushan.,...&Su, Zhengchang.(2019).Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples.ADVANCED SCIENCE,6(4),9.
MLA	Gao, Bo,et al."Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples".ADVANCED SCIENCE 6.4(2019):9.