Messenger RNAs (mRNAs) fulfil specific biological roles in cells and, thus, their expression may be adapted to suit specific circumstances. This is in part achieved through selective gene transcription and post-transcriptional events, the regulation of which must be tightly integrated and controlled. To comprehensively study the coordinated effects of transcriptional and post-transcriptional regulatory elements, and to obtain coherent results, it is advisable to use different methodologies. Adequately integrating the data derived from these distinct methodologies then becomes critical to elucidating the relationships between the coordinated cellular effects assayed, particularly when applied to normal and disease states. Such integrated studies are likely to be particularly useful to identify markers suitable for early detection of diseases and to devise strategies for therapeutic interventions. Throughout this chapter, we will focus on the methods currently available to analyse mRNA and microRNA (miRNA) expression, paying special attention to the influence of miRNAs on mRNA metabolism. We will introduce miARma-Seq, a comprehensive pipeline that facilitates the simultaneous integration of mRNA and miRNA expression data. For illustrative purposes, we include a case study that incorporates data from RNASeq and small-RNASeq, detailing all the steps necessary to define the differential expression of both mRNA- and miRNA-encoding genes. Finally, we explore the possible regulatory relationships that drive significant and potentially relevant changes in mRNA and miRNA gene expression.

中文翻译：

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miARma-Seq，一个用于同时研究和整合 miRNA 和 mRNA 表达数据的综合管道

信使 RNA (mRNA) 在细胞中发挥特定的生物学作用，因此，它们的表达可能会适应特定环境。这部分是通过选择性基因转录和转录后事件实现的，它们的调节必须紧密整合和控制。为了全面研究转录和转录后调控元件的协同效应，并获得一致的结果，建议使用不同的方法。充分整合源自这些不同方法的数据对于阐明所分析的协调细胞效应之间的关系至关重要，尤其是在应用于正常和疾病状态时。此类综合研究可能对识别适合早期检测疾病的标志物和设计治疗干预策略特别有用。在本章中，我们将重点介绍目前可用于分析 mRNA 和 microRNA (miRNA) 表达的方法，特别关注 miRNAs 对 mRNA 代谢的影响。我们将介绍 miARma-Seq，这是一个综合管道，可促进 mRNA 和 miRNA 表达数据的同时整合。出于说明目的，我们包含了一个案例研究，其中包含来自 RNASeq 和小 RNASeq 的数据，详细说明了定义 mRNA 和 miRNA 编码基因的差异表达所需的所有步骤。最后，