Figure 7. Identification of genome-wide alternative splicing (AS) events in HeLa cells.

A: Pie chart of differentially regulated AS events, total 384 (FDR≤ 5%, Δψ≥ 15%, n=3) between untreated versus TGF-β and EGF treated cells (72hrs). SE: skipped exon; RI: retained intron; MXE: mutually excluded exons; A5SS: alternative 5’ splice site; A3SS: alternative 3’ splice site. The number of exon inclusion and exon skipping SE events is also listed.

B: Ingenuity pathway analyses of affected genes identified in A. Signaling pathways that are associated with EMT and cell movement are significantly enriched. P-value (-log10) is indicated on the X-axis. Cut off (p≤0.02) is shown by a dash line in the graph.

C: Venn diagram of overlapping skipped exon (SE) events between those induced by the combined TGF-β and EGF treatment and by TWIST overexpression. The 163 SE events (Shapiro et al, 2011) were used in comparison because analyzing the original RNA-seq data using our analysis pipeline yielded much smaller number of SE events.

D: Representative RNA-seq reads at the CD44 locus. T+E: cells treated with TGF-β and EGF for 72 hr. Orange rectangle marks the position of the variable exon region.

E: Number of differentially regulated AS events induced by TGF-β and EGF treatment in HeLa cells stably expressing shNS, shPCBP1 or shSMAD3 vector.

F: qRT-PCR validation of nine SE events. Ratios of alternative exon versus constant exon of individual gene are shown as mean ± S.D. (n=3), and * denotes statistical significance (p<0.02) between treated (72 hr) and untreated samples.

See also Figure S7.