Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns

doi:10.3389/fgene.2018.00194

CSpace > 应用数学研究所

	Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns
	Chen, Jinyu 1,2; Zhang, Shihua1,2,3
	2018-05-29
发表期刊	FRONTIERS IN GENETICS
ISSN	1664-8021
卷号	9 页码:12
摘要	The increasing availability of high-throughput biological data, especially multi-dimensional genomic data across the same samples, has created an urgent need for modular and integrative analysis tools that can reveal the relationships among different layers of cellular activities. To this end, we present a MATLAB package, Matrix Integration Analysis (MIA), implementing and extending four published methods, designed based on two classical techniques, non-negative matrix factorization (NMF), and partial least squares (PLS). This package can integrate diverse types of genomic data (e.g., copy number variation, DNA methylation, gene expression, microRNA expression profiles, and/or gene network data) to identify the underlying modular patterns by each method. Particularly, we demonstrate the differences between these two classes of methods, which give users some suggestions about how to select a suitable method in the MIA package. MIA is a flexible tool which could handle a wide range of biological problems and data types. Besides, we also provide an executable version for users without a MATLAB license.
关键词	bioinformatics multi-dimensional genomics matrix integrative analysis data integration module discovery non-negative matrix factorization (NMF) partial least squares (PLS)
DOI	10.3389/fgene.2018.00194
语种	英语
资助项目	National Natural Science Foundation of China[11131009] ; National Natural Science Foundation of China[61379092] ; National Natural Science Foundation of China[61422309] ; National Natural Science Foundation of China[61621003] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Chinese Academy of Sciences[KFZD-SW-219] ; National Key Research and Development Program of China[2017YFC0908405] ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000433387900001
出版者	FRONTIERS MEDIA SA
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/30399
专题	应用数学研究所
通讯作者	Zhang, Shihua
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS,CEMS, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Chen, Jinyu,Zhang, Shihua. Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns[J]. FRONTIERS IN GENETICS,2018,9:12.
APA	Chen, Jinyu,&Zhang, Shihua.(2018).Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns.FRONTIERS IN GENETICS,9,12.
MLA	Chen, Jinyu,et al."Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns".FRONTIERS IN GENETICS 9(2018):12.