Coughlan Sean J, Agrawal Vikas, Meyers Blake
Agilent Technologies Inc., Little Falls Site, 2850 Centerville Road, Wilmington, DE 19808- 1644, USA. sean
Comp Funct Genomics. 2004;5(3):245-52. doi: 10.1002/cfg.397.
Microarrays and tag-based transcriptional profiling technologies represent diverse but complementary data types. We are currently conducting a comparison of high-density in situ synthesized microarrays and massively-parallel signature sequencing (MPSS) data in the model plant, Arabidopsis thaliana. The MPSS data (available at http://mpss.udel.edu/at) and the microarray data have been compiled using the same RNA source material. In this review, we outline the experimental strategy that we are using, and present preliminary data and interpretations from the transcriptional profiles of Arabidopsis leaves and roots. The preliminary data indicate that the log ratio differences of transcripts between leaves and roots measured by microarray data are in better agreement with the MPSS data than the absolute intensities measured for individual microarrays hybridized to only one of the cRNA populations. The correlation was substantially improved by focusing on a subset of genes excluding those with very low expression levels; this selection may have removed noisy data. Future reports will incorporate more than 10 tissues that have been sampled by MPSS.
微阵列和基于标签的转录谱分析技术代表了不同但互补的数据类型。我们目前正在模式植物拟南芥中对高密度原位合成微阵列和大规模平行签名测序（MPSS）数据进行比较。MPSS数据（可在http://mpss.udel.edu/at获取）和微阵列数据是使用相同的RNA源材料汇编而成的。在本综述中，我们概述了正在使用的实验策略，并展示了来自拟南芥叶和根转录谱的初步数据及解读。初步数据表明，与仅与一种cRNA群体杂交的单个微阵列所测量的绝对强度相比，通过微阵列数据测量的叶和根之间转录本的对数比差异与MPSS数据的一致性更好。通过关注排除低表达水平基因的基因子集，相关性得到了显著改善；这种选择可能去除了噪声数据。未来的报告将纳入通过MPSS采样的10多个组织。
