Simultaneous dimension reduction and adjustment for confounding variation

doi:10.1073/pnas.1617317113

CSpace > 应用数学研究所

	Simultaneous dimension reduction and adjustment for confounding variation
	Lin, Zhixiang 1; Yang, Can 2; Zhu, Ying 3,4; Duchi, John 1,5; Fu, Yao 6; Wang, Yong7 ; Jiang, Bai 1; Zamanighomi, Mahdi 1; Xu, Xuming 4; Li, Mingfeng 4; Sestan, Nenad 4,8,9; Zhao, Hongyu 3; Wong, Wing Hung 1,10
	2016-12-20
发表期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN	0027-8424
卷号	113 期号:51 页码:14662-14667
摘要	Dimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biological or technical in origin. In this study, we extend principal component analysis (PCA) to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding (AC) variation. We show that ACPCA can adjust for (i) variations across individual donors present in a human brain exon array dataset and (ii) variations of different species in a model organism ENCODE RNA sequencing dataset. Our approach is able to recover the anatomical structure of neocortical regions and to capture the shared variation among species during embryonic development. For gene selection purposes, we extend AC-PCA with sparsity constraints and propose and implement an efficient algorithm. The methods developed in this paper can also be applied to more general settings.
关键词	dimension reduction confounding variation transcriptome
DOI	10.1073/pnas.1617317113
语种	英语
资助项目	National Science Foundation[DMS-1106738] ; National Institutes of Health[R01 GM59507] ; National Institutes of Health[P01 CA154295] ; National Institutes of Health[R01 HG007834] ; National Institutes of Health[R01 GM109836] ; National Institutes of Health[P50 MH106934] ; National Institutes of Health[U01 MH103339] ; National Science Funding of China[61501389] ; Hong Kong Research Grant Council[22302815] ; Hong Kong Research Grant Council[12316116] ; Hong Kong Baptist University[FRG2/14-15/069] ; Hong Kong Baptist University[FRG2/15-16/011]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000390044900050
出版者	NATL ACAD SCIENCES
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/24410
专题	应用数学研究所
通讯作者	Zhao, Hongyu; Wong, Wing Hung
作者单位	1.Stanford Univ, Dept Stat, Stanford, CA 94305 USA 2.Hong Kong Baptist Univ, Dept Math, Kowloon Tong, Hong Kong, Peoples R China 3.Yale Sch Publ Hlth, Dept Biostat, New Haven, CT 06520 USA 4.Yale Sch Med, Kavli Inst Neurosci, Dept Neurosci, New Haven, CT 06510 USA 5.Stanford Univ, Dept Elect Engn, Stanford, CA 94305 USA 6.Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06511 USA 7.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 8.Yale Sch Med, Dept Genet, New Haven, CT 06510 USA 9.Yale Sch Med, Program Cellular Neurosci Neurodegenerat & Repair, Comparat Med Sect, Dept Psychiat, New Haven, CT 06510 USA 10.Stanford Univ, Dept Hlth Res & Policy, Stanford, CA 94305 USA
推荐引用方式 GB/T 7714	Lin, Zhixiang,Yang, Can,Zhu, Ying,et al. Simultaneous dimension reduction and adjustment for confounding variation[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2016,113(51):14662-14667.
APA	Lin, Zhixiang.,Yang, Can.,Zhu, Ying.,Duchi, John.,Fu, Yao.,...&Wong, Wing Hung.(2016).Simultaneous dimension reduction and adjustment for confounding variation.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,113(51),14662-14667.
MLA	Lin, Zhixiang,et al."Simultaneous dimension reduction and adjustment for confounding variation".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113.51(2016):14662-14667.