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.

引用

页数：18

共 65 条

[51] Genome-wide approaches to studying chromatin modifications
Schones, Dustin E.
Zhao, Keji
[J]. NATURE REVIEWS GENETICS, 2008, 9 (03) : 179 - 191
[52] Signaling network model of chromatin
Schreiber, SL
Bernstein, BE
[J]. CELL, 2002, 111 (06) : 771 - 778
[53] The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
Schübeler, D
MacAlpine, DM
Scalzo, D
Wirbelauer, C
Kooperberg, C
van Leeuwen, F
Gottschling, DE
O'Neill, LP
Turner, BM
Delrow, J
Bell, SP
Groudine, M
[J]. GENES & DEVELOPMENT, 2004, 18 (11) : 1263 - 1271
[54] Genome regulation by polycomb and trithorax proteins
Schuettengruber, Bernd
Chourrout, Daniel
Vervoort, Michel
Leblanc, Benjamin
Cavalli, Giacomo
[J]. CELL, 2007, 128 (04) : 735 - 745
[55] Divergent Transcription from Active Promoters
Seila, Amy C.
Calabrese, J. Mauro
Levine, Stuart S.
Yeo, Gene W.
Rahl, Peter B.
Flynn, Ryan A.
Young, Richard A.
Sharp, Phillip A.
[J]. SCIENCE, 2008, 322 (5909) : 1849 - 1851
[56] Is there a code embedded in proteins that is based on post-translational modifications?
Sims, Robert J., III
Reinberg, Danny
[J]. NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2008, 9 (10) : 815 - 820
[57] The language of covalent histone modifications
Strahl, BD
Allis, CD
[J]. NATURE, 2000, 403 (6765) : 41 - 45
[58] Crosstalk among Histone Modifications
Suganuma, Tamaki
Workman, Jerry L.
[J]. CELL, 2008, 135 (04) : 604 - 607
[59] MRG-1, an autosome-associated protein, silences X-linked genes and protects germline immortality in Caenorhabditis elegans
Takasaki, Teruaki
Liu, Zheng
Habara, Yasuaki
Nishiwaki, Kiyoji
Nakayama, Jun-ichi
Inoue, Kunio
Sakamoto, Hiroshi
Strome, Susan
[J]. DEVELOPMENT, 2007, 134 (04): : 757 - 767
[60] Defining an epigenetic code
Turner, Bryan M.
[J]. NATURE CELL BIOLOGY, 2007, 9 (01) : 2 - 6

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