Figure 5
Integrated analysis of miRNA and mRNA expression: (a) Number of miRNA in all identified disease-associated transcripts (upper panel, gray bar) or in each group of identified disease-associated transcripts. Lower panel shows relative enrichment (observed vs expected) of miRNA in each of the defined disease-associated groups. White labels correspond to BH-corrected p values of a hypergeometric test. (b) Log2 CPM expression of miRNA identified in all four groups of disease-associated transcripts (black dots). Black line denotes median log2 CPM. Boxplot lower and upper hinges correspond to the first and third quartiles respectively. Whiskers extend to the largest expression value no further than 1.5 interquartile range from the hinge. Outliers are shown in transparent gray. (c) Barplot of BH-adjusted p values [− log10] of miRNA target enrichment analysis for each of the four identified groups of disease-associated genes (left panel). Only miRNA with significant enrichment of their target genes in any of the four defined groups of disease-associated mRNA are shown. Dashed line indicates the level of significance chosen (BH-adjusted p value < 0.05). Right panel shows BH-adjusted p values [− log10] of a Kolmogorov–Smirnov test for negative skew in correlation between miRNA and target mRNA expression (Orange: Macula samples, Blue: Periphery samples). (d) Distribution of Spearman correlation values between miR-30a-5p and its putative target genes in either macula (upper panel) or periphery samples (right panel). Dashed line corresponds to background distribution of 100.000 correlations between non-associated miRNA/mRNA pairs. Middle panel represents the scatter plot for individual Spearman correlation values between miR-30a-5p and its targets.
