This repository contains all analyses and figure scripts used in ''Dissection of the role of a Scr Homology 3 domain in the evolution of binding preference of paralogous proteins ''.
PCA_analysisX.R scripts are used for the analysis of raw PCA data (output of pyphe-quant). The scripts are used to threshold, scale and save the data for subsequent visualization. There is one PCA_analysis script for each of the three PCA experiments described in the paper.
PCA_SH3_dependency.R is used to test if the interactions are different between the paralog variants. It uses Wilcoxon tests( Benjamin-Hochberg correction) to test if the extant paralogs show different PPI scores than other paralog variants. The significant tests between the extant paralog and the SH3-depleted variant indicate the PPIs which are SH3-dependent.
FigureX.R and FigureSX.R are scripts to visualize the results, create the figures and supplementary figures of the paper. Some supplementary panels and figures are generated in FigureX.R, PCA_analysisX.R scripts, and PCA_SH3_dependency.R.