Figure 2.

Coordination between AS events belonging to the same genes. (a) The correlation between the alternative splicing (AS) levels of pairs of alternative exons belonging to the same genes was assessed using standard Spearman correlation. The cumulative distribution plot shows the number of exon pairs (y-axis) observed to have an absolute value standard Spearman correlation higher than the value given on the x-axis. The blue curve with closed circles represents the number of observed exon pairs from the same gene above a given correlation threshold. The red curve with open circles is the average number of random pairs above a given correlation threshold, as determined using permutation resampling analysis (see Additional data file 1 [Materials and methods]). Also, representative examples of pairs of alternative exons with correlated splicing levels are shown (b) for a pair of exons with positively correlating inclusion levels from the Exo70 gene and (c) for a pair of exons with negatively correlating inclusion levels from the Neo1 gene. Upper panels show plots comparing the GenASAP percentage exon exclusion levels for each exon in a correlating pair, with the percentage exclusion levels for each exon separately plotted on the y-axis and x-axis. Circle sizes indicate relative transcript levels for the corresponding gene in each tissue shown, with larger circles indicating higher transcript levels. Lower panels show radioactive reverse transcription polymerase chain reaction (RT-PCR) assays performed with primer pairs targeted to constitutive exons flanking each alternative exon in a correlated pair. Percentage exclusion levels for each alternative exon, as measured using a phosphorimager (see Materials and methods), are shown. Additional examples of correlated pairs of exons validated by RT-PCR assays are shown in Additional data file 1 [Figure 2]. ES, embryonic stem cells.