(
a) Principal components analysis of protein (left panel) and RNA (right panel) profiles of 202 iPSC lines, with individual lines color coded by disease status. In total 6583 proteins detected in all 202 cell lines and 16,852 genes with RNA expression (TPM >1) in at least 30 lines were considered. (
b) Differential expression analysis between the largest disease entities (Bardet-Biedl;N = 38 and Monogenic diabetes; N = 38 and ‘Normal’; N = 112;
Supplementary file 2) for protein (left panels) and RNA (right panels). p-Values and effect size estimates obtained from a linear model with the disease indicator as an exogenous variable are shown. For protein, the fold change is computed for each batch and averaged across batches. Significantly differential RNA or protein levels (FDR < 10%, Benjamini-Hochberg adjusted) are indicated in red.