Fig. 3
Targets of miR-1199-5p function during an EMT. a Overall gene expression regulation by miR-1199-5p during a TGFβ-induced EMT. RNA-sequencing analysis was performed on NMuMG/E9 cells transiently transfected with a miR-1199-5p or a negative control (miR-Ctr) mimic. Cells were cultured for 4 days in the presence (4 days; miR-Ctr- and miR-1199-5p-transfected cells) or absence of TGFβ (only miR-Ctr-transfected cells). The scatterplot depicts overall gene expression (log2FC) anti-correlation between miR-1199-5p 4 days vs. miR-Ctr 4 days over miR-Ctr 4 days vs. miR-Ctr 0 days. Differential expression analysis (red dashed line: log2FC(±1); False Discovery Rate (FDR) <0.05) identified 787 genes regulated by miR-1199-5p during an EMT. Green quadrant: increased gene expression; red quadrant: decreased gene expression. b Functional annotation clustering analysis of differentially expressed genes from a. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by DAVID for the top five biological processes (top), pathways (bottom) and their associated P and Benjamini–Hochberg values. c Identification of miR-1199-5p direct targets in EMT. The Venn diagram depicts the number of genes differentially expressed upon miR-1199-5p expression during an EMT (blue), predicted direct targets of miR-1199-5p by miRWalk2.0 (red) and the number of overlapping genes. Sixty-six out of 90 genes demonstrate a downregulation in their expression upon forced expressed of miR-1199-5p in EMT, including the EMT TF Zeb1
