what does the positive or negative of PSI means

Question

[gengyang12138]

I had analysis the alternative splicing of genes, and got the ΔPSI. I set the threshold of differential AS event as |ΔPSI| > 0.05. But I don't know the difference between positive and negative of ΔPSI.

Answer 1

[Kristoffer Vitting-Seerup]

ΔPSI indicate the changes in how much a genomic feature is used.

If we consider the an example of an exon inclusion/exclusion when comparing two conditions (cond1 and cond2) then a postive ΔPSI indicate that the exon is included more frequently in cond2 (compared to cond1) while a negative ΔPSI indicate it is included less frequently in cond2 (again compared to cond1).

Please note that:

1. A ΔPSI cutoff of 0.05 migth be quite low - you definitively want to have a statistical test on top.
2. Analysis of alternative splicing can both be done at exon or AS-event level (with tools such as DEXSeq, Miso and SUPPA2) and at isoform level (with tools such as my R package IsoformSwitchAnalyzeR) which also allows for prediction of functional consequences.

Hope this helps. Kristoffer