Department of Biology, University of Padova, 35121 Padova, Italy.
Nucleic Acids Res. 2010 Apr;38(7):e97. doi: 10.1093/nar/gkp1239. Epub 2010 Jan 13.
MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interactions.
微小 RNA（miRNA）是小的非编码 RNA，通过与靶 mRNA 3'UTR 区域的不完全结合，在转录后和翻译水平上调节基因表达。虽然 miRNA-mRNA 相互作用的从头计算预测仍然存在重大挑战，但通过仔细整合 miRNA 和 mRNA 的配对表达谱到分析中，可以克服其一些局限性。在这项工作中，我们展示了为微阵列平台选择适当的探针注释是实现 miRNA-mRNA 相互作用识别的良好敏感性的必要条件。我们比较了使用基于基因和基于转录本的定制 CDF（我们为多种不同注释（ENSEMBL、RefSeq、AceView）开发的 CDF）分析相同表达谱时获得的结果。在所有情况下，基于转录本的注释都明显提高了数据集成的有效性，从而更可靠地证实了计算预测的 miRNA-mRNA 相互作用。
