title: High-dimensional genomic data bias correction and data integration using MANCIE.
abstract: High-dimensional genomic data analysis is challenging due to noises and biases in high-throughput experiments. We present a computational method matrix analysis and normalization by concordant information enhancement (MANCIE) for bias correction and data integration of distinct genomic profiles on the same samples. MANCIE uses a Bayesian-supported principal component analysis-based approach to adjust the data so as to achieve better consistency between sample-wise distances in the different profiles. MANCIE can improve tissue-specific clustering in ENCODE data, prognostic prediction in Molecular Taxonomy of Breast Cancer International Consortium and The Cancer Genome Atlas data, copy number and expression agreement in Cancer Cell Line Encyclopedia data, and has broad applications in cross-platform, high-dimensional data integration.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: Chongzhi
authors.initials: C
authors.lastname: Zang
authors.affiliation: Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.|Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
authors.forename: Tao
authors.identifier: http://orcid.org/0000-0002-4355-149X
authors.initials: T
authors.lastname: Wang
authors.affiliation: Center for Statistical Science, Tsinghua University, Beijing 100084, China.
authors.forename: Ke
authors.initials: K
authors.lastname: Deng
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Statistics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai 200092, China.
authors.forename: Sheng'en
authors.initials: S
authors.lastname: Hu
authors.affiliation: Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai 200092, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qin
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215, USA.
authors.forename: Tengfei
authors.initials: T
authors.lastname: Xiao
authors.affiliation: National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
authors.forename: Shihua
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: Clifford A
authors.initials: CA
authors.lastname: Meyer
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215, USA.|Department of Medical Biophysics, University of Toronto, Toronto, Ontatio M5G 1L7, Canada.
authors.forename: Housheng Hansen
authors.identifier: http://orcid.org/0000-0003-2898-3363
authors.initials: HH
authors.lastname: He
authors.affiliation: Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02215, USA.
authors.forename: Myles
authors.initials: M
authors.lastname: Brown
authors.affiliation: Department of Statistics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.affiliation: Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.|Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.|Simons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.|Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D045744:Cell Line, Tumor; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D012984:Software; D013223:Statistics as Topic