Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data

doi:10.1155/2015/573956

	Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data
	Wang, Yishu 1; Yang, Dejie 2; Deng, Minghua 1,3,4
	2015
发表期刊	BIOMED RESEARCH INTERNATIONAL
ISSN	2314-6133
页码	11
摘要	Background. Epistatic miniarray profile (EMAP) studies have enabled the mapping of large-scale genetic interaction networks and generated large amounts of data in model organisms. One approach to analyze EMAP data is to identify gene modules with densely interacting genes. In addition, genetic interaction score (S score) reflects the degree of synergizing or mitigating effect of two mutants, which is also informative. Statistical approaches that exploit both modularity and the pairwise interactions may provide more insight into the underlying biology. However, the high missing rate in EMAP data hinders the development of such approaches. To address the above problem, we adopted the matrix decomposition methodology "low-rank and sparse decomposition" (LRSDec) to decompose EMAP data matrix into low-rank part and sparse part. Results. LRSDec has been demonstrated as an effective technique for analyzing EMAP data. We applied a synthetic dataset and an EMAP dataset studying RNA-related processes in Saccharomyces cerevisiae. Global views of the genetic cross talk between different RNA-related protein complexes and processes have been structured, and novel functions of genes have been predicted.
DOI	10.1155/2015/573956
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31171262] ; National Natural Science Foundation of China[31471246] ; National Natural Science Foundation of China[31428012] ; National Key Basic Research Project of China[2015CB910303]
WOS研究方向	Biotechnology & Applied Microbiology ; Research & Experimental Medicine
WOS类目	Biotechnology & Applied Microbiology ; Medicine, Research & Experimental
WOS记录号	WOS:000359224400001
出版者	HINDAWI PUBLISHING CORPORATION
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/9497
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Deng, Minghua
作者单位	1.Peking Univ, Ctr Quantitat Biol, Beijing 100871, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 3.Peking Univ, Sch Math Sci, Beijing 100871, Peoples R China 4.Peking Univ, Ctr Stat Sci, Beijing 100871, Peoples R China
推荐引用方式 GB/T 7714	Wang, Yishu,Yang, Dejie,Deng, Minghua. Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data[J]. BIOMED RESEARCH INTERNATIONAL,2015:11.
APA	Wang, Yishu,Yang, Dejie,&Deng, Minghua.(2015).Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data.BIOMED RESEARCH INTERNATIONAL,11.
MLA	Wang, Yishu,et al."Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data".BIOMED RESEARCH INTERNATIONAL (2015):11.