Fig. 1

Assessment and properties of exons differentially spliced between cell lines K562 and Gm12878. a Classification of ‘more included’ and ‘less included’ exons. b Estimated inclusion ratio in the K562 cell line (x-axis) and in the Gm12878 cell line (y-axis) of exons whose inclusion is: (1) significantly higher in Gm12878 (dark blue); (2) significantly higher in the K562 cell line (dark red); (3) whose inclusion does not change significantly between the two cell lines (light blue). c Distribution of the sum of the strengths of 5’ and 3’ splice sites flanking exons that do not display significant differences in inclusion between the cell lines (notAS, left boxplot) and differentially included (that is, regulated) exons (AS, right boxplot). Wilcoxon rank-sum tests were calculated for the two distributions, significance levels are indicated: * (0.05 > P > 0.01), ** (0.01 > P > 0.001), *** (0.001 > P). d Exon length distribution of AS and notAS exons. e Fraction of AS and notAS exons, the length of which is multiple of three: only exons that were entirely coding were considered. f Expression of genes with exons whose inclusion is: (1) significantly higher in Gm12878 (dark blue); (2) significantly higher in the K562 cell line (dark red). X-axis: log2 (TSS-HMM value) in K562; Y-axis: log2 (TSS-HMM value) in Gm12878. g Experimental validation: comparison between inclusion levels of differentially regulated exons between Gm12878 and K562, calculated analyzing RNASeq ENCODE data (gray bars) or with RT-qPCR analyses of RNA extracted from K562 and Gm12878 (green bars). For RT-qPCR analysis were used primers amplifying specifically the inclusion or skipping isoform. Gray bars represent log2 ratio of inclusion level between Gm12878 and K562 calculated for each exon form RNASeq. Green bars represent log2 ratio between inclusion/skipping ratio in Gm12878 and K562, normalized to the ratio in a constitutive exon on the same transcript; error bars represent standard deviations of three independent experiments. Twelve out of 15 exons tested show consistent inclusion direction as measured by RNASeq and RT-qPCR