PCA, K-means, and VAT of miRNAs.

The common identifier (“gga-miR”) for all the miRNA-exon Ensembl IDs was removed for legibility. All miRbase IDs in the plots are followed by a hyphen and the correspond exon number. (A) A PCA of the UCSC-verified miRNA-containing exons in our dataset (excluding gga-miR-3064 exon 1). Repeated miRNA IDs are due to a miRNA spanning more than one exon. Note that positive fold-changes are down-regulated exons, and negative fold-changes are up-regulated exons. (B) K-means clustering (k = 3 clusters) of all UCSC-verified miRNA exons, ellipses are drawn using Euclidean distance (excluding gga-miR-3064 exon 1). (C) A heatmap representation of the visual assessment of cluster tendency for all miRNA exons. Red corresponds to high similarity, and blue corresponds to low similarity.