Fig. 6

Global transcriptome and in silico analysis-based miR-342-3p target gene identification. a Schematic representation of combined microarray-based and computational miR-342-3p target gene identification. b Network visualization of Gene Ontology enrichment analysis of genes differentially expressed in miR-342-3p-transfected RAW264.7 mouse macrophages (FDR ≤0.01) using the ClueGO Cytoscape plugin. Nodes represent enriched GO biological process terms, node colors represent corresponding FDR values (Benjamini-Hochberg method), and node sizes represent the number of genes associated with the GO term. Only the label of the most significant term per group is shown. Nodes without second degree connections are omitted for clarity. c Sylamer analysis revealed that only miR-342-3p 8-mer seed matches were enriched among downregulated genes in miR-342-3p-transfected macrophages compared with miR-negative control-treated cells. miR-342-3p and murine miRNA seed matches are represented as red dashed lines and gray lines, respectively. d Cumulative distributions of relative change (t-statistic) for different sets of potential miR-342-3p target genes with 7mer.1A (blue), 7mer.m8 (green), and 8-mer (red) seeds or the top 1000 TargetScan (orange) or microT-CDS (purple) and TargetExpress (brown) predictions to be functionally downregulated. Set size and the statistical significance of each set being more repressed than genes with no potential target site are shown in parentheses