Cargando…
High-dimensional genomic data bias correction and data integration using MANCIE
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 t...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833864/ https://www.ncbi.nlm.nih.gov/pubmed/27072482 http://dx.doi.org/10.1038/ncomms11305 |
_version_ | 1782427397360975872 |
---|---|
author | Zang, Chongzhi Wang, Tao Deng, Ke Li, Bo Hu, Sheng'en Qin, Qian Xiao, Tengfei Zhang, Shihua Meyer, Clifford A. He, Housheng Hansen Brown, Myles Liu, Jun S. Xie, Yang Liu, X. Shirley |
author_facet | Zang, Chongzhi Wang, Tao Deng, Ke Li, Bo Hu, Sheng'en Qin, Qian Xiao, Tengfei Zhang, Shihua Meyer, Clifford A. He, Housheng Hansen Brown, Myles Liu, Jun S. Xie, Yang Liu, X. Shirley |
author_sort | Zang, Chongzhi |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4833864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-48338642016-05-02 High-dimensional genomic data bias correction and data integration using MANCIE Zang, Chongzhi Wang, Tao Deng, Ke Li, Bo Hu, Sheng'en Qin, Qian Xiao, Tengfei Zhang, Shihua Meyer, Clifford A. He, Housheng Hansen Brown, Myles Liu, Jun S. Xie, Yang Liu, X. Shirley Nat Commun Article 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. Nature Publishing Group 2016-04-13 /pmc/articles/PMC4833864/ /pubmed/27072482 http://dx.doi.org/10.1038/ncomms11305 Text en Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Zang, Chongzhi Wang, Tao Deng, Ke Li, Bo Hu, Sheng'en Qin, Qian Xiao, Tengfei Zhang, Shihua Meyer, Clifford A. He, Housheng Hansen Brown, Myles Liu, Jun S. Xie, Yang Liu, X. Shirley High-dimensional genomic data bias correction and data integration using MANCIE |
title | High-dimensional genomic data bias correction and data integration using MANCIE |
title_full | High-dimensional genomic data bias correction and data integration using MANCIE |
title_fullStr | High-dimensional genomic data bias correction and data integration using MANCIE |
title_full_unstemmed | High-dimensional genomic data bias correction and data integration using MANCIE |
title_short | High-dimensional genomic data bias correction and data integration using MANCIE |
title_sort | high-dimensional genomic data bias correction and data integration using mancie |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833864/ https://www.ncbi.nlm.nih.gov/pubmed/27072482 http://dx.doi.org/10.1038/ncomms11305 |
work_keys_str_mv | AT zangchongzhi highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT wangtao highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT dengke highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT libo highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT hushengen highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT qinqian highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT xiaotengfei highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT zhangshihua highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT meyerclifforda highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT hehoushenghansen highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT brownmyles highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT liujuns highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT xieyang highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie AT liuxshirley highdimensionalgenomicdatabiascorrectionanddataintegrationusingmancie |