MADS+: discovery of differential splicing events from Affymetrix exon junction array data

Alternative 3'/5' splice site is the inclusion or skipping of the extended part of the exon.

HJAY_Plot_alt35.pdf contains the graphs of alternative 3'/5' splice site exons. The red lines in the figure represent the gene expression indexes. The blue lines in the figure represent the probe intensities.

For alternative 3'/5' splice sites, shorter_juc=exon-exon junction probeset of shorter isoform, longer_juc=exon-exon junction probeset of longer isoform, shorter_ex=exon probeset of shorter isoform and longer_ex=exon probeset of longer isoform. In which, shorter exon-exon junction probeset and shorter exon probeset are probesets for the shorter isoform of alternative 3'/5' splice sites. Longer exon-exon junction probeset and longer exon probeset are the probesets for the extended isoform of alternative 3'/5' splice sites.

The numbers below shorter_juc, longer_juc, shorter_ex and longer_ex are the p values for each probeset with directions. Positive p values indicate more inclusion levels in second group of samples. Negative p values indicate less inclusion levels in second group of samples. 

HJAY_excel_alt35.txt contains the gene names, coordinates and p values in spreadsheet.