A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

被引：107

作者：

Cheng, Chao ^{[1
]}

Yan, Koon-Kiu ^{[1
]}

Yip, Kevin Y. ^{[1
,2
]}

Rozowsky, Joel ^{[1
]}

Alexander, Roger ^{[1
]}

Shou, Chong ^{[1
]}

Gerstein, Mark ^{[1
,3
,4
]}

机构：

[1] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[2] Chinese Univ Hong Kong, Dept Comp Sci & Engn, Shatin, Hong Kong, Peoples R China

[3] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

[4] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 02期

关键词：

GENOME-WIDE MAPS; HISTONE MODIFICATIONS; TRANSCRIPTION ELONGATION; CAENORHABDITIS-ELEGANS; STERILE-20; KINASE; X-CHROMOSOME; CODE; DNA; ACETYLATION; PROMOTERS;

D O I：

10.1186/gb-2011-12-2-r15

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We develop a statistical framework to study the relationship between chromatin features and gene expression. This can be used to predict gene expression of protein coding genes, as well as microRNAs. We demonstrate the prediction in a variety of contexts, focusing particularly on the modENCODE worm datasets. Moreover, our framework reveals the positional contribution around genes (upstream or downstream) of distinct chromatin features to the overall prediction of expression levels.

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页数：18

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