Personalized characterization of diseases using sample-specific networks

doi:10.1093/nar/gkw772

	Personalized characterization of diseases using sample-specific networks
	Liu, Xiaoping 1,2; Wang, Yuetong 1,3; Ji, Hongbin1,4 ; Aihara, Kazuyuki 2; Chen, Luonan1,2,4
	2016-12
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	44 期号:22
发表状态	已发表
DOI	10.1093/nar/gkw772
摘要	A complex disease generally results not from malfunction of individual molecules but from dysfunction of the relevant system or network, which dynamically changes with time and conditions. Thus, estimating a condition-specific network from a single sample is crucial to elucidating the molecular mechanisms of complex diseases at the system level. However, there is currently no effective way to construct such an individual-specific network by expression profiling of a single sample because of the requirement of multiple samples for computing correlations. We developed here with a statistical method, i.e. a sample-specific network (SSN) method, which allows us to construct individual-specific networks based on molecular expressions of a single sample. Using this method, we can characterize various human diseases at a network level. In particular, such SSNs can lead to the identification of individual-specific disease modules as well as driver genes, even without gene sequencing information. Extensive analysis by using the Cancer Genome Atlas data not only demonstrated the effectiveness of the method, but also found new individual-specific driver genes and network patterns for various types of cancer. Biological experiments on drug resistance further validated one important advantage of our method over the traditional methods, i.e. we can even identify such drug resistance genes that actually have no clear differential expression between samples with and without the resistance, due to the additional network information.
收录类别	SCI
语种	英语
资助项目	JSPS KAKENHI[15H05707]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000395742900004
出版者	OXFORD UNIV PRESS
WOS关键词	RENAL-CELL CARCINOMA ; PROTEIN-PROTEIN INTERACTIONS ; CYCLIN B1 ; CANCER ; GENE ; P53 ; EXPRESSION ; ONCOPROTEIN ; MEDICINE ; MUC1
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/1608
专题	生命科学与技术学院_特聘教授组_季红斌组生命科学与技术学院_特聘教授组_陈洛南组
通讯作者	Ji, Hongbin; Aihara, Kazuyuki; Chen, Luonan
作者单位	1.Chinese Acad Sci, CAS Ctr Excellence Mol Cell Sci, Innovat Ctr Cell Signaling Network, Key Lab Syst Biol,Inst Biochem & Cell Biol,Shangh, Shanghai 200031, Peoples R China 2.Univ Tokyo, Inst Ind Sci, Tokyo 1538505, Japan 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 200031, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Liu, Xiaoping,Wang, Yuetong,Ji, Hongbin,et al. Personalized characterization of diseases using sample-specific networks[J]. NUCLEIC ACIDS RESEARCH,2016,44(22).
APA	Liu, Xiaoping,Wang, Yuetong,Ji, Hongbin,Aihara, Kazuyuki,&Chen, Luonan.(2016).Personalized characterization of diseases using sample-specific networks.NUCLEIC ACIDS RESEARCH,44(22).
MLA	Liu, Xiaoping,et al."Personalized characterization of diseases using sample-specific networks".NUCLEIC ACIDS RESEARCH 44.22(2016).