Identification of miRNA-mRNA Co-expression by network analysis in dengue virus infection

Dengue virus (DENV), transmitted by Aedes mosquitoes, causes various illnesses, from mild dengue fever to severe dengue hemorrhagic fever and dengue shock syndrome. Understanding the molecular mechanisms underlying DENV infection is crucial for developing effective diagnostics and treatments. This study integrates mRNA and miRNA sequencing data to explore the regulatory networks involved in DENV infection. Samples from both DENV-infected and control conditions were analyzed. Differential expression analysis identified significantly altered genes and miRNAs. Target genes of differentially expressed miRNAs (DEMs) were identified using miRNet. Metascape is used to perform the functional enrichment analysis of target genes. Employing Pearson correlation analysis, potential regulatory relationships between miRNAs and mRNAs were determined. Receiver Operating Characteristic (ROC) analysis assessed the diagnostic potential of key miRNA-mRNA pairs. Differential expression analysis revealed a distinct set of Differentially Expressed Genes (DEGs) and miRNAs. Functional enrichment analysis indicated that upregulated genes were involved in processes such as DNA-templated transcription and cell division, while downregulated genes were associated with TNF-alpha signaling and blood vessel development. Pearson correlation analysis highlighted key negatively correlated miRNA-mRNA pairs. ROC analysis demonstrated high diagnostic potential for pairs such as TUBA1A-hsa-mir-205-5p, CXCL16-hsa-mir-205-5p, MED29-hsa-mir-148b-5p, PPARA-hsa-mir-3614-5p, and PTPRJ-hsa-mir-96-5p, with Area Under the Curve (AUC) values of 1. The study provides valuable insights into the miRNA-mRNA regulatory networks in DENV infection, identifying potential therapeutic targets and diagnostic key genes. The identified miRNA-mRNA interactions offer promising avenues for developing targeted therapies and improving DENV diagnostics, contributing to better management of dengue virus infections.

The online version contains supplementary material available at 10.1007/s13337-025-00915-z.