Fig. 2

Alternative transcription, splicing, and polyadenylation are highly interdependent. a Bar charts illustrate the number and proportion of genes that show significant coupling in MCF-7 cells. Genes with TSS- or PAS-coupled features are also presented. b Venn diagram shows the number of genes with various types of coupling representing interdependencies between different alternative processes. The total number of mutually inclusive and exclusive networks are also listed. c Histogram of the relative positions of TSSs with (blue) and without (gray) significant coupling to mRNA processing events. Relative positions are calculated based on the length of the total exonic sequence at each locus. Scatter plot shows the fraction of significantly coupled TSSs (blue) to alternative exons (black) and PASs (red), plotted at each relative position. d Histogram of the relative positions of alternative exons with (brown) and without (gray) significant coupling to other exons. Scatter plot shows the fraction of significantly coupled exons to other exons, plotted at each relative position. e Histogram of the relative positions of PASs with (red) and without (gray) significant coupling to alternative transcription and splicing events. Scatter plot shows the fraction of significantly coupled PASs (red) to alternative TSSs (blue) and exons (black), plotted at each relative position. For plots depicting the percentage of linked features per position, the bin size of 0.02 was used