Table 4:

Overview of Bioinformatics Tools and Processes in miRNA Research and Analysis.

Aspect	Tools	Tools	References
Identification and Quantification of miRNAs	miRDeep2, miRExpress	miRDeep2, miRExpress	[111]
miRNA Target Prediction	TargetScan, miRanda	TargetScan, miRanda	[112]
miRNA-mRNA Interaction and Network Analysis	DIANA-TarBase, miRTarBase	DIANA-TarBase, miRTarBase	[113]
Functional Enrichment Analysis	DIANA-mirPath, miRWalk	DIANA-mirPath, miRWalk	[114]
Differential Expression Analysis	edgeR, DESeq	Utilizing statistical models, identify miRNAs with significant expression changes across various conditions.	[115]
Data Integration and Visualization	Cytoscape, miRBase	Integrate and visualize miRNA, mRNA, and protein interaction data to gain greater insight into complex regulatory networks.	[116]
Example of Usage in Cancer Research	miRDeep2, edgeR, TargetScan, DIANA-mirPath, Cytoscape	Gather RNA-Seq data from cancerous/normal tissues; identify and quantify miRNAs; compare expression levels among gene targets; analyze differential expression and target gene targeting patterns, as well as visualize interaction networks.	[117]