Pathway analysis

The top 13 differentially expressed miRNAs with raw p-value less than 0.05 were chosen for pathway enrichment analysis. DIANA-miRPath (20) and in-house developed Python scripts were used for pathway analysis. For each miRNA, a set of target genes was created with a threshold of prediction score 0.7 against micro CDS target prediction database. The union set comprising all 13 sets of target gene was mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to derive significantly enriched pathways using Fisher’s exact test. Two heatmaps, miRNA-by-sample and miRNA-by-pathway, were drawn with DIANA-miRPath. Among these, <Pathways In Cancer>, which had 121 genes targeted by 8 miRNAs, was selected for visualization. Cytoscape (21) was used to draw miRNA-gene interaction plot. GeneMANIA (22) was used to infer gene-gene interaction on top of miRNA-gene interaction. Two interaction plots were merged into a single graph.