Fig. 4
Expression and genomic features of CGs for HCT116 unstranded libraries. See Supplementary Figs. 30, 33 for HCT116 stranded and 184hTERT data set plots. a CG ∆PSI boxplots, per T3 treatment concentration. b Boxplots of FPKM values for CG upstream and downstream participants, compared to all genes with FPKM ≥ 1 (i.e., expressed genes). c Boxplots of interrupted indices for CGs across T3 concentrations. Interrupted indices are calculated as the ratio of coverage between the portions of a gene retained and removed by CGs (Supplementary Fig. 32a). Boxplots are shown for the upstream and downstream CG participants. d Boxplots of splicing indices for CGs across T3 concentrations. Splicing indices are calculated as the number of concordant read pairs spanning a CG splice junction in a CG participant, divided by the number of CG splice junction spanning reads that support the presence of a CG (Supplementary Fig. 32b). Boxplots are shown for the upstream and downstream CG participants. e Density plot of CG splice junction distances vs. gene distances in the genome. f Density plot of CG splice junction distances vs. intron lengths of multi-exonic protein coding genes in the genome. g Density plot of CG participant distances vs. consecutive gene distances in the genome. h Barplots showing the number of CG splice junctions falling within different annotated gene locations, across T3 concentrations. Barplots for the upstream and downstream CG participants are shown. i Boxplots of intron lengths for introns adjacent to the upstream and downstream CG splice junction, and all introns in upstream and downstream CG gene partners
