KMS Of Academy of mathematics and systems sciences, CAS
| Simultaneous dimension reduction and adjustment for confounding variation | |
Lin, Zhixiang1; Yang, Can2; Zhu, Ying3,4; Duchi, John1,5; Fu, Yao6; Wang, Yong7 ; Jiang, Bai1; Zamanighomi, Mahdi1; Xu, Xuming4; Li, Mingfeng4; Sestan, Nenad4,8,9; Zhao, Hongyu3; Wong, Wing Hung1,10
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| 2016-12-20 | |
| Source Publication | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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| ISSN | 0027-8424 |
| Volume | 113Issue:51Pages:14662-14667 |
| Abstract | 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. |
| Keyword | dimension reduction confounding variation transcriptome |
| DOI | 10.1073/pnas.1617317113 |
| Language | 英语 |
| Funding Project | 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 Research Area | Science & Technology - Other Topics |
| WOS Subject | Multidisciplinary Sciences |
| WOS ID | WOS:000390044900050 |
| Publisher | NATL ACAD SCIENCES |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/24410 |
| Collection | 应用数学研究所 |
| Corresponding Author | Zhao, Hongyu; Wong, Wing Hung |
| Affiliation | 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 |
| Recommended Citation 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. |
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