Genome-wide prediction of DNase I hypersensitivity using gene expression
dc.contributor.author | Zhou, Weiqiang | |
dc.contributor.author | Sherwood, Ben | |
dc.contributor.author | Ji, Zhicheng | |
dc.contributor.author | Xue, Yingchao | |
dc.contributor.author | Du, Fang | |
dc.contributor.author | Bai, Jiawei | |
dc.contributor.author | Ying, Mingyao | |
dc.contributor.author | Ji, Hongkai | |
dc.date.accessioned | 2018-11-12T22:51:41Z | |
dc.date.available | 2018-11-12T22:51:41Z | |
dc.date.issued | 2017-10-19 | |
dc.identifier.citation | Zhou, W., Sherwood, B., Ji, Z., Xue, Y., Du, F., Bai, J., ... & Ji, H. (2017). Genome-wide prediction of DNase I hypersensitivity using gene expression. Nature communications, 8(1), 1038. | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/27310 | |
dc.description.abstract | We evaluate the feasibility of using a biological sample’s transcriptome to predict its genome-wide regulatory element activities measured by DNase I hypersensitivity (DH). We develop BIRD, Big Data Regression for predicting DH, to handle this high-dimensional problem. Applying BIRD to the Encyclopedia of DNA Elements (ENCODE) data, we found that to a large extent gene expression predicts DH, and information useful for prediction is contained in the whole transcriptome rather than limited to a regulatory element’s neighboring genes. We show applications of BIRD-predicted DH in predicting transcription factor-binding sites (TFBSs), turning publicly available gene expression samples in Gene Expression Omnibus (GEO) into a regulome database, predicting differential regulatory element activities, and facilitating regulome data analyses by serving as pseudo-replicates. Besides improving our understanding of the regulome–transcriptome relationship, this study suggests that transcriptome-based prediction can provide a useful new approach for regulome mapping. | en_US |
dc.description.sponsorship | R01HG006282 | en_US |
dc.description.sponsorship | R01HG006841 | en_US |
dc.description.sponsorship | 2012-MSCRFE-0135-00 | en_US |
dc.publisher | Nature Research | en_US |
dc.rights | This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. | en_US |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_US |
dc.title | Genome-wide prediction of DNase I hypersensitivity using gene expression | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Sherwood, Ben | |
kusw.kudepartment | Business | en_US |
dc.identifier.doi | 10.1038/s41467-017-01188-x | en_US |
dc.identifier.orcid | https://orcid.org/0000-0001-9396-9571 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-6480-0141 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.rights.accessrights | openAccess | en_US |
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