Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA.
Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
BMC Bioinformatics. 2020 Jul 6;21(Suppl 4):247. doi: 10.1186/s12859-020-3436-7.
Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the miRNA-mRNA pairs between tumor and normal samples is still not resolved, and this hinders the potential clinical applications. There is an urgent need to develop innovative methodologies and tools that can characterize and visualize functional consequences of cancer risk gene and miRNA pairs while analyzing the tumor and normal samples simultaneously.
We developed an innovative bioinformatics tool for visualizing functional annotation of miRNA-mRNA pairs in a network, known as MMiRNA-Viewer. The tool takes mRNA and miRNA interaction pairs and visualizes mRNA and miRNA regulation network. Moreover, our MMiRNA-Viewer web server integrates and displays the mRNA and miRNA gene annotation information, signaling cascade pathways and direct cancer association between miRNAs and mRNAs. Functional annotation and gene regulatory information can be directly retrieved from our web server, which can help users quickly identify significant interaction sub-network and report possible disease or cancer association. The tool can identify pivotal miRNAs or mRNAs that contribute to the complexity of cancer, while engaging modern next-generation sequencing technology to analyze the tumor and normal samples concurrently. We compared our tools with other visualization tools.
Our MMiRNA-Viewer serves as a multitasking platform in which users can identify significant interaction clusters and retrieve functional and cancer-associated information for miRNA-mRNA pairs between tumor and normal samples. Our tool is applicable across a range of diseases and cancers and has advantages over existing tools.
虽然有许多研究使用 miRNA 和 mRNA 测序数据来研究 miRNA-mRNA 相互作用的特征，但肿瘤和正常样本中 miRNA-mRNA 对相关系数和表达值变化的复杂性仍未得到解决，这阻碍了其潜在的临床应用。因此，迫切需要开发创新的方法和工具，以便在同时分析肿瘤和正常样本时，能够对癌症风险基因和 miRNA 对的功能后果进行特征描述和可视化。
我们开发了一种名为 MMiRNA-Viewer 的创新生物信息学工具，用于可视化 miRNA-mRNA 对在网络中的功能注释。该工具采用 mRNA 和 miRNA 相互作用对，并可视化 mRNA 和 miRNA 调控网络。此外，我们的 MMiRNA-Viewer 网络服务器整合并显示了 mRNA 和 miRNA 基因注释信息、信号级联途径以及 miRNAs 和 mRNAs 之间的直接癌症关联。功能注释和基因调控信息可以直接从我们的网络服务器中检索，这有助于用户快速识别重要的相互作用子网络，并报告可能的疾病或癌症关联。该工具可以识别对癌症复杂性有贡献的关键 miRNA 或 mRNA，同时利用现代下一代测序技术同时分析肿瘤和正常样本。我们将我们的工具与其他可视化工具进行了比较。
我们的 MMiRNA-Viewer 是一个多功能平台，用户可以在其中识别显著的相互作用簇，并检索肿瘤和正常样本中 miRNA-mRNA 对的功能和癌症相关信息。我们的工具适用于多种疾病和癌症，并且优于现有工具。
