Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA.
BMC Genomics. 2012 Nov 15;13:629. doi: 10.1186/1471-2164-13-629.
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.
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，这两种方法定量的转录组相关性很好。然而，它们都没有考虑到它们各自的优缺点是否可以互补。解决这个问题的关键要求是了解一个众所周知的数据集。在这方面，来自病原菌的 HrpX 调控组是一个理想的选择，因为 HrpX 转录因子的靶基因由于其在致病性中的核心作用而得到了很好的研究。
我们通过对 γ-变形菌黄单胞菌亚种黄单胞菌的野生型和 hrpX 突变菌株的转录组进行分析，比较了 RNA-seq 和微阵列在检测已知 HrpX 靶基因方面的性能。我们的比较分析表明，RNA-seq 和微阵列定量的基因表达水平在绝对值和相对水平上都很好地相关（Spearman 相关系数 rs>0.76）。此外，RNA-seq 和微阵列定量的差异表达基因（DEGs）的表达水平与 qRT-PCR 定量也很好地相关（rs=0.58 至 0.94）。最后，除了新鉴定的 55 个 DEGs 外，RNA-seq 和微阵列还检测到了 72%的已知 HrpX 靶基因，而其余 28%的靶基因只能通过两种方法中的一种检测到。
这项研究显著提高了我们对关键转录因子 HrpX 调控组的理解。RNA-seq 和微阵列共同提供了一个更全面的 HrpX 调控组图谱，独特地鉴定了新的 DEGs。我们的研究表明，RNA-seq 和微阵列在转录组分析中相互补充。
