Overlapping clustering of gene expression data using penalized weighted normalized cut

doi:10.1002/gepi.22164

CORC > 上海财经大学 > 上海财经大学

	Overlapping clustering of gene expression data using penalized weighted normalized cut
	Hidalgo, Sebastian J. Teran 1; Zhu, Tingyu 2; Wu, Mengyun 1,3; Ma, Shuangge 1
刊名	GENETIC EPIDEMIOLOGY
	2018-12
卷号	42 期号:8 页码:796-811
关键词	gene expression data NCut overlapping clustering penalization
ISSN号	0741-0395
DOI	10.1002/gepi.22164
英文摘要	Clustering has been widely conducted in the analysis of gene expression data. For complex diseases, it has played an important role in identifying unknown functions of genes, serving as the basis of other analysis, and others. A common limitation of most existing clustering approaches is to assume that genes are separated into disjoint clusters. As genes often have multiple functions and thus can belong to more than one functional cluster, the disjoint clustering results can be unsatisfactory. In addition, due to the small sample sizes of genetic profiling studies and other factors, there may not be sufficient evidence to confirm the specific functions of some genes and cluster them definitively into disjoint clusters. In this study, we develop an effective overlapping clustering approach, which takes account into the multiplicity of gene functions and lack of certainty in practical analysis. A penalized weighted normalized cut (PWNCut) criterion is proposed based on the NCut technique and an L2 norm constraint. It outperforms multiple competitors in simulation. The analysis of the cancer genome atlas (TCGA) data on breast cancer and cervical cancer leads to biologically sensible findings which differ from those using the alternatives. To facilitate implementation, we develop the function pwncut in the R package NCutYX.
WOS研究方向	Genetics & Heredity ; Mathematical & Computational Biology
语种	英语
出版者	WILEY
WOS记录号	WOS:000450354800004
内容类型	期刊论文
源URL	[http://10.2.47.112/handle/2XS4QKH4/465]
专题	上海财经大学
作者单位	1.Yale Univ, Dept Biostat, New Haven, CT 06520 USA; 2.Xiamen Univ, Dept Stat, Xiamen, Peoples R China; 3.Shanghai Univ Finance & Econ, Sch Stat & Management, Shanghai 200433, Peoples R China
推荐引用方式 GB/T 7714	Hidalgo, Sebastian J. Teran,Zhu, Tingyu,Wu, Mengyun,et al. Overlapping clustering of gene expression data using penalized weighted normalized cut[J]. GENETIC EPIDEMIOLOGY,2018,42(8):796-811.
APA	Hidalgo, Sebastian J. Teran,Zhu, Tingyu,Wu, Mengyun,&Ma, Shuangge.(2018).Overlapping clustering of gene expression data using penalized weighted normalized cut.GENETIC EPIDEMIOLOGY,42(8),796-811.
MLA	Hidalgo, Sebastian J. Teran,et al."Overlapping clustering of gene expression data using penalized weighted normalized cut".GENETIC EPIDEMIOLOGY 42.8(2018):796-811.