Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
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发表时间：
2010
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通讯作者：
D. Betel;Anjali J. Koppal;P. Agius;C. Sander;C. Leslie
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作者：
D. Betel;Anjali J. Koppal;P. Agius;C. Sander;C. Leslie
通过分析预测的microRNA:：目标位点比对的AU组成、3 '结合和UTR位置特征，计算上下文得分值。种子特异性得分采用Grimson等人描述的回归参数计算。表S6[8]使用从[39]下载的源代码。在我们的研究中，miRNA::target alignments的预测miRNA::target alignments是由miRanda生成的，由于预测miRNA::target alignments的差异，基于我们的预测双工（mirSVR-CS）计算的上下文得分值与TargetScan （TargetScanCS）计算的上下文得分值并不完全相同，这种差异可能会对性能评估产生一定影响。为了评估我们计算的上下文分数与TargetScan5.0提供的上下文分数之间差异的显著性，我们首先计算了Linsley数据集[21]中典型站点的两个上下文分数值之间的Pearson相关性。我们发现两个分数之间存在显著的相关性（补充表1），大部分差异可归因于3 '结合分数的变化。我们还将这两个分数与观察到的对数表达变化联系起来，发现mirSVR-CS值实际上比TargetScan提供的上下文分数与观察到的表达变化联系得更好。我们得出结论，在我们的比较分析中，预测miRNA::mRNA双链碱基配对的差异，以及由此产生的上下文评分值的差异，并没有对上下文评分的表现产生不利影响。
Context score values were computed by parsing the AU composition, 3’-binding and UTR position features from predicted microRNA::target site alignments. Seed specific scores were calculated using the regression parameters described in Grimson et al. Table S6 [8] using the source code downloaded from [39]. Due to differences in predicted miRNA::target alignments, which in our study were generated by miRanda, the context score values computed based on our predicted duplexes (mirSVR-CS) are not exactly the same as those calculated by TargetScan (TargetScanCS), and this difference may have some impact on the performance assessment. To assess the significance of the differences between our computed context scores to those provided by TargetScan5.0, we first calculated the Pearson correlation between the two context score values for the canonical sites in the Linsley data set [21]. We found a significant correlation between the two scores (Supplementary Table 1), and most of the difference can be attributed to variations in the 3’-binding scores. We also correlated the two scores with the observed log expression changes and found that mirSVR-CS values are in fact better correlated with the observed expression changes than the context scores provided by TargetScan. We conclude that differences in predicting the base-pairing in the miRNA::mRNA duplexes, and the resulting differences in context score values, did not adversely affect context score performance in our comparative analysis.