Extended Data Fig. 9: Analysis of Ago2 seCLIP clusters.
From: Gain-of-function mutation of microRNA-140 in human skeletal dysplasia
a, Hexamer enrichment analysis in all Ago2-bound seCLIP clusters including intronic clusters identified in WT (left) and mutant (right) chondrocytes (WT, n = 14,947 clusters; G/G, n = 13,873 clusters). The x axis shows z-scores of hexamer frequency. The y axis shows the negative log10 P value from two-sided Fisher’s exact test with Bonferroni correction of the hexamer enrichment above background. b, Hexamer enrichment analysis for various genomic annotations. The negative log10 P values from one-sided Fisher’s exact test with Bonferroni correction of the hexamer enrichment above background are shown. Left (Ago2 WT): 5′ UTR clusters, n = 279; CDS clusters, n = 1,315; 3′ UTR clusters, n = 1,782; intronic clusters, n = 10,402; non-coding RNA region clusters, n = 434; others, n = 735. Right (Ago2 G/G): 5′ UTR clusters, n = 303; CDS clusters, n = 2,006; 3′ UTR clusters, n = 3,229; intronic clusters, n = 7,091; non-coding RNA region clusters, n = 332; others, n = 912. c, Cumulative distributions of fold changes of mRNAs with Ago2-bound seCLIP CDS clusters with the ACCACC motif in mutant chondrocytes (red) or Ago2-bound seCLIP CDS clusters with the ACCACU motif in WT chondrocytes. P values (versus a control gene set) were calculated by one-sided Kolmogorov–Smirnov test for either direction: upregulation (U) or downregulation (D) with Bonferroni correction (control genes, n = 10,093; miR-140-5p-WT, n = 28; miR-140-5p-G, n = 100).
