Effect of trans-factor binding on RNA processing shifts.

A) and D) show models of hypothesized mechanism of splicing or transcription factor influence on RNA processing and exon usage. B) An example of a correlation between the changes in gene expression of an RNA processing factor (LARP7) and the percent of RIs that shift towards the intron retention across all environments for which gene expression could be assessed. E) An example of a correlation between the changes in gene expression of a transcription factor (HSF1) and the percent of AFEs that shift towards the upstream AFE across all environments for which gene expression could be assessed. The correlation for B) and E) was tested using Spearman’s rho and the p-value shown is Benjamini-Hochberg corrected while the trendline depicts the best-fit line. C) Graph indicating the predictability (AUC as a proxy) of SE or RI shifts in a certain environment given predicted splicing factor binding sites (RNAcompete). F) Graph indicating the predictability (AUC as a proxy) of AFE shifts in a certain environment given transcription factor footprints [48].