A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
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DOI：
10.1093/nar/gks804
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发表时间：
2012-11-01
影响因子：
14.9
通讯作者：
Nielsen J
中科院分区：
文献类型：
--
作者：
Nookaew I;Papini M;Pornputtapong N;Scalcinati G;Fagerberg L;Uhlén M;Nielsen J
RNA - seq最近已成为转录组研究中一种颇具吸引力的首选方法，与微阵列相比具有若干优势。在本研究中，我们试图评估使用Illumina平台产生的RNA - seq数据进行分析时所涉及的不同分析步骤的作用，并基于通过Affymetrix微阵列获得的结果进行跨平台比较。作为我们工作的一个案例研究，我们使用了酿酒酵母（Saccharomyces cerevisiae）菌株CEN.PK 113 - 7D，使其在两种不同条件（分批培养和恒化培养）下生长。在此，我们评估了遗传变异对基因表达水平估计的影响，使用了三种不同的比对工具（Gsnap、Stampy和TopHat）将读数比对到S288c基因组上，还评估了五种不同的统计方法（baySeq、Cuffdiff、DESeq、edgeR和NOISeq）检测差异基因表达的能力，并且我们探究了使用参考基因组的RNA - seq分析和从头组装方法之间的一致性。据报道，生物学重复之间具有高重复性（相关性≥0.99），两个平台在基因表达水平分析上具有高度一致性（相关性≥0.91）。不同统计方法得出的差异基因表达鉴定结果以及基于基因本体注释的综合分析结果都很吻合。总体而言，我们的研究为基因表达分析提供了两种平台（RNA - seq和微阵列）之间有用且全面的比较，并阐述了RNA - seq数据分析中所涉及的不同步骤的作用。
RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation ≥0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation ≥0.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
16.6
作者：
Canelas, Andre B.;Harrison, Nicola;Nielsen, Jens
通讯作者：
Nielsen, Jens
影响因子：
7
作者：
Lunter, Gerton;Goodson, Martin
通讯作者：
Goodson, Martin
影响因子：
3.7
作者：
Mudge, Joann;Miller, Neil A.;Khrebtukova, Irina;Lindquist, Ingrid E.;May, Gregory D.;Huntley, Jim J.;Luo, Shujun;Zhang, Lu;van Velkinburgh, Jennifer C.;Farmer, Andrew D.;Lewis, Sharon;Beavis, William D.;Schilkey, Faye D.;Virk, Selene M.;Black, C. Forrest;Myers, M. Kathy;Mader, Lar C.;Langley, Ray J.;Utsey, John P.;Kim, Ryan W.;Roberts, Rosalinda C.;Khalsa, Sat Kirpal;Garcia, Meredith;Ambriz-Griffith, Victoria;Harlan, Richard;Czika, Wendy;Martin, Stanton;Wolfinger, Russell D.;Perrone-Bizzozero, Nora I.;Schroth, Gary P.;Kingsmore, Stephen F.
通讯作者：
Kingsmore, Stephen F.