在动物和植物基因组中普遍存在着一类长度大约为22nt的用于转录后调控的非编码RNA——microRNAs (miRNAs)。miRNAs通过完全或不完全的碱基互补绑定到信使RNA（mRNA）上通过抑制翻译或者直接导致mRNA降解的方式来调节靶基因的表达。为了研究miRNAs在转录水平上面的调控作用，Lim等人把两种人类基因组中组织特异的miRNAs（miR-1和miR-124）转染到海拉细胞中，并通过microarray分析转染前后细胞中各基因mRNA表达水平的变化情况，结果表明动物基因组中靶基因与miRNAs不完全的碱基互补也会导致mRNA的直接降解。通过分析他们提供的mRNA表达水平变化的数据，我们发现这两个miRNAs各自的靶基因mRNA表达水平的下调倍数有着明显的差别。于是我们认为这些靶基因mRNA序列本身应该存在某些影响其受调节程度的因素，为此我们提取和分析这些靶基因mRNA的序列特征，通过对这些序列特征与mRNA表达水平下调数据进行统计分析，发现miRNA靶基因受调节的程度与以下几个因素相关联：mRNA序列中miRNA靶位点的个数、靶位点与miRNAs序列碱基互补的程度、 以及绑定后形成二级结构的稳定程度（即最低自由能的大小）。在此基础上，我们初步建立起一个多因子作用下的miRNA 靶基因mRNA表达水平下调程度模型，分析表明：该模型基本上反映了一部分因素对于miRNA靶基因mRNA表达水平下调程度的影响。

MicroRNAs (miRNAs) are small non-coding RNAs that serve as post-transcriptional regulators of gene expression in plants and animals. They act by binding to complementary sites on target mRNAs to induce cleavage or repression of productive translation. To investigate the influence of miRNAs on transcript levels, Lim .et al transfected two miRNAs (miR-1 and miR-124) into human cells and used microarrays to examine changes in the messenger RNA profile. In each case, there was many genes downregulated. By analyzing their results, we found that the fold decreases of these targets were different remarkably. There should be several different factors that act on the degree of the decrease of target genes expression simultaneously. We extracted and analyzed three types of sequence signatures of these targets: the number of binding sites, the position of binding sites, the sequence match level between miRNA and binding sites, the free energy of optimal strand-strand interaction between miRNA and binding sites, and found that, statistically, the three signatures are all associated with the down-regulation effects on the target genes expression level. Finally we proposed a model according these signatures, and this model has been proved to be able to reflect the degree of the decrease of target genes expression.