Figure 4
Differential expression analysis of microRNAs during development. (A) Principal component analysis (PCA) of microRNA expression in each replicate and time-point. Four replicates are shown for each time-point. (B) Heatmap of all-versus-all pairwise Spearman correlation coefficients between time-points. Numbers in tiles are r values, and heatmap colour coding is based on r value. (C) Heatmap showing z-score calculated for expression of each microRNA through embryonic development. Each microRNA is classified into an expression cluster, indicated by the colour coded ribbon. (D) Expression profiles for microRNAs with membership scores ≥ 0.6 for each cluster; the number indicated in parentheses is the total number of microRNAs belonging to each cluster. (E) Composition of the 4 expression clusters in newly annotated and previously annotated microRNAs. Chi-squared tests were performed for each cluster. Cluster 1 shows a significantly higher proportion of newly annotated microRNAs than expected, X2 (1, N = 61) = 14.95, p = 1.10 × 10–4, whereas cluster 4 contains an unexpectedly high proportion of conserved microRNAs, X2 (1, N = 92) = 19.40, p = 1.05 × 10–5, p-value significance levels are indicated by asterisks.
