MIMR: Development of a Web-Based System for miRNA and mRNA Integrated Analysis

The human body is a complex network of systems that is harmonized with multiple biological components. To understand these interactions is very challenging. With rapid development of advanced sequencing technologies, massive amounts of data such as mRNA, miRNA are rapidly accumulated. The integrated analysis of mRNA-miRNA has brought an extensive understanding of complex biological systems and pathological mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that intricately regulate target gene products, resulting in the inhibition of gene expression. While these miRNAs play crucial roles in essential biological processes-ranging from immunity and metabolism to cell death-their specific impacts on diseases remain unknown. Recent studies have been focused on the integration of miRNA and mRNA expression to reveal the underlying biological pathways and mechanisms responsible for disease manifestation. We proposed a novel approach for integrative analysis of miRNA and mRNA expression data and developed MIMR (Integrative Analysis of miRNA and mRNA), a web-based application that leverages the Random Walk with Restart (RWR) algorithm. MIMR incorporates both direct and indirect interactions by utilizing protein-protein interaction (PPI) networks and experimentally validated mRNA-miRNA target interactions. MIMR provides comprehensive results, including novel pathological pathways associated with a specific disease and interactive network diagrams representing the mRNAs and miRNAs. We applied it to Alzheimer and breast cancer data and successfully identified the novel biological pathways related to these diseases. In summary, MIMR will offer a deeper insight into the hidden mechanisms of diseases and identify potential therapeutic strategies through integrated analysis of miRNAs and mRNAs.