RNA-seq and microarray complement each other in transcriptome profiling.
RNA-seq and microarray complement each other in transcriptome profiling.
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DOI：
10.1186/1471-2164-13-629
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发表时间：
2012-11-15
期刊：
影响因子：
4.4
通讯作者：
Wang N
中科院分区：
文献类型：
--
作者：
Kogenaru S;Qing Y;Guo Y;Wang N
RNA-seq和微阵列是用于全基因组转录组分析的两种常用方法。目前的比较研究表明，这两种方法量化的转录组具有良好的相关性。然而，考虑到它们固有的优势和局限性，它们都没有解决它们是否互补的问题。解决这个问题的关键要求是对已知数据集的了解。在这方面，来自病原菌的HrpX规则组是一个理想的选择，因为HrpX转录因子的靶基因在致病性中的核心作用被研究得很好。我们通过分析γ-变形菌黄单胞菌（Xanthomonas citri subsp）野生型和HrpX突变株的转录组，比较了RNA-seq和微阵列检测已知HrpX靶基因的能力。citri。我们的比较分析表明，RNA-seq和微阵列量化的基因表达水平在绝对水平和相对水平上都具有良好的相关性（Spearman相关系数，rs 0.76）。此外，RNA-seq和微阵列定量的显著差异表达基因（DEGs）的表达水平也与基于qRT-PCR的定量呈正相关（rs = 0.58 ~ 0.94）。最后，除了55个新鉴定的deg外，已知的HrpX靶基因中有72%被RNA-seq和微阵列同时检测到，而剩下的28%只能被两种方法中的任何一种检测到。这项研究大大提高了我们对关键转录因子HrpX的规律的理解。RNA-seq和微阵列通过独特地识别新的deg，共同提供了HrpX规则组的更全面的图像。我们的研究表明，RNA-seq和微阵列在转录组分析中是互补的。
RNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Current comparison studies have shown that transcriptome quantified by these two methods correlated well. However, none of them have addressed if they complement each other, considering the strengths and the limitations inherent with them. The pivotal requirement to address this question is the knowledge of a well known data set. In this regard, HrpX regulome from pathogenic bacteria serves as an ideal choice as the target genes of HrpX transcription factor are well studied due to their central role in pathogenicity. We compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of γ-Proteobacterium Xanthomonas citri subsp. citri. Our comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray well-correlated both at absolute as well as relative levels (Spearman correlation-coefficient, rs > 0.76). Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes (DEGs) also well-correlated with qRT-PCR based quantification (rs = 0.58 to 0.94). Finally, in addition to the 55 newly identified DEGs, 72% of the already known HrpX target genes were detected by both RNA-seq and microarray, while, the remaining 28% could only be detected by either one of the methods. This study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. RNA-seq and microarray together provide a more comprehensive picture of HrpX regulome by uniquely identifying new DEGs. Our study demonstrated that RNA-seq and microarray complement each other in transcriptome profiling.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
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：
3.2
作者：
Astua-Monge, G;Freitas-Astua, J;Machado, MA
通讯作者：
Machado, MA
影响因子：
3.5
作者：
Fenselau, S;Bonas, U
通讯作者：
Bonas, U
DOI：
10.1093/bioinformatics/btp101
发表时间：
2009-04-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Bindea G;Mlecnik B;Hackl H;Charoentong P;Tosolini M;Kirilovsky A;Fridman WH;Pagès F;Trajanoski Z;Galon J
通讯作者：
Galon J