Calculation of PSI expression ratio between two groups of transcripts

ADAS-viewer provides for analyses on the basis of either transcript expression (as TPM) or exon expression (as percent spliced in, PSI) in the context of AS events such as exon skipping, intron retention, alternative 5′ splice site use, and alternative 3′ splice site use. PSI values can be calculated using TPM values, and are estimated in a three-step process: (1) separating transcripts of a single gene into two groups: one with the splicing event and the other without; (2) summarizing expression (TPM) for each group, and (3) taking the ratio of the sums of the two groups as the PSI value. In other words, PSI (ψ_t) is estimated according to the equation proposed by IVAS³⁸, a Bioconductor package for investigating alternative splicing, as follows:

where Xi and Xs indicate the transcript group with and without the alternatively spliced exon, respectively. ADAS-viewer uses this PSI value to perform analyses using WGS, methylation, and miRNA data.