Improving RNA-Seq expression estimates by correcting for fragment bias

被引：1190

作者：

Roberts, Adam ^{[1
]}

Trapnell, Cole ^{[2
,3
]}

Donaghey, Julie ^{[2
]}

Rinn, John L. ^{[2
,3
]}

Pachter, Lior ^{[1
,4
,5
]}

机构：

[1] Univ Calif Berkeley, Dept Comp Sci, Berkeley, CA 94720 USA

[2] 7 Cambridge Ctr, Broad Inst, Cambridge, MA 02142 USA

[3] Harvard Univ, Dept Stem Cell & Regenerat Biol, Cambridge, MA 02138 USA

[4] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA

[5] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 03期

关键词：

GENE-EXPRESSION; DIFFERENTIAL EXPRESSION; SPLICE JUNCTIONS; REVEALS;

D O I：

10.1186/gb-2011-12-3-r22

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：

The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.

引用

页数：14

共 30 条

[1] Differential expression analysis for sequence count data [J].

Anders, Simon ;

Huber, Wolfgang .

GENOME BIOLOGY, 2010, 11 (10)

[2]

Armour CD, 2009, NAT METHODS, V6, P647, DOI [10.1038/NMETH.1360, 10.1038/nmeth.1360]

[3] Detection of splice junctions from paired-end RNA-seq data by SpliceMap [J].

Au, Kin Fai ;

Jiang, Hui ;

Lin, Lan ;

Xing, Yi ;

Wong, Wing Hung .

NUCLEIC ACIDS RESEARCH, 2010, 38 (14) :4570-4578

[4] rQuant.web: a tool for RNA-Seq-based transcript quantitation [J].

Bohnert, Regina ;

Raetsch, Gunnar .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W348-W351

[5] A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling [J].

Bradford, James R. ;

Hey, Yvonne ;

Yates, Tim ;

Li, Yaoyong ;

Pepper, Stuart D. ;

Miller, Crispin J. .

BMC GENOMICS, 2010, 11

[6]

Bühlmann P, 1999, ANN STAT, V27, P480

[7] Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments [J].

Bullard, James H. ;

Purdom, Elizabeth ;

Hansen, Kasper D. ;

Dudoit, Sandrine .

BMC BIOINFORMATICS, 2010, 11

[8]

Fleige Simone, 2006, Molecular Aspects of Medicine, V27, P126, DOI 10.1016/j.mam.2005.12.003

[9] Ensembl 2011 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Chen, Yuan ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Kokocinski, Felix ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Overduin, Bert ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Rios, Daniel ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Spudich, Giulietta ;

Tang, Y. Amy ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

Vilella, Albert J. ;

White, Simon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Zamora, Jorge ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Parker, Anne ;

Proctor, Glenn .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D800-D806

[10] Direct multiplexed measurement of gene expression with color-coded probe pairs [J].

Geiss, Gary K. ;

Bumgarner, Roger E. ;

Birditt, Brian ;

Dahl, Timothy ;

Dowidar, Naeem ;

Dunaway, Dwayne L. ;

Fell, H. Perry ;

Ferree, Sean ;

George, Renee D. ;

Grogan, Tammy ;

James, Jeffrey J. ;

Maysuria, Malini ;

Mitton, Jeffrey D. ;

Oliveri, Paola ;

Osborn, Jennifer L. ;

Peng, Tao ;

Ratcliffe, Amber L. ;

Webster, Philippa J. ;

Davidson, Eric H. ;

Hood, Leroy .

NATURE BIOTECHNOLOGY, 2008, 26 (03) :317-325

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