作为转录组调控的重要角色，微小RNA能够有效地扩散体细胞突变对广泛细胞过程的影响，并最终表现为疾病的发生和预后的决定。之前的研究试图将突变与基因表达失调相关联时，忽略了与不均等样本大小和不平衡类别平衡情况相关的众多假阳性。为了正确解决这个问题，我们开发了一个统计框架，严格评估了突变对微小RNA的影响程度，与一个匹配的样本结构的基于排列的零分布相对比。在一个全癌症研究中执行该框架，我们确定了9008个蛋白编码基因对miRNA有统计显著的突变影响。其中，83个基因的集体miRNA表达在九种癌症类型中表现出了显著的预后能力。例如，在低级别胶质瘤中，有10个基因的突变广泛影响了miRNA，并且所有这些基因的miRNA表达都与其对应的预后有关。我们的框架还通过功能分析进行了验证，并增加了丰富的功能，包括分析miRNA亚型的能力；聚合预后分析；先进的注释，如突变类型、调控因子变化、体细胞模体和疾病关系；以及启示性的可视化，如突变OncoPrint、Ideogram和交互式mRNA-miRNA网络。详细数据可在Bioinformatics在线访问，网址为http://innovebioinfo.com/Database/TmiEx/MutMix.php。© The Author(s) 2023. Published by Oxford University Press.

As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios.To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA-miRNA network.http://innovebioinfo.com/Database/TmiEx/MutMix.php.Supplementary data are available at Bioinformatics online.© The Author(s) 2023. Published by Oxford University Press.