Fig. 4

Paralog switches often mediate protein complex composition during reprogramming. a Twenty-three paralog pairs were found to be co-regulated at least at one time point. The majority of them had fold changes of opposite sign indicating paralog switches. Protein profiles across the five time points of the reprogramming are shown for two representative examples. Dots indicate the average value of independent reprogramming experiments performed in two replicates for protein profiles [12] and one to three replicates (per time point) for gene expression profiles [22]. Red dots indicate significant cases (adjusted p value <0.05, see Methods for details). D indicates the number of days after the induction of the reprogramming factors (D0). b The same paralog switches in the chromatin remodeling complex BAF that we identified during reprogramming were also found to be affected during stem cell differentiation by Ho et al. [27]. We identified 14 additional paralog switches affecting among others the COPII complex. Red and green colors indicate up- and downregulated complex members, respectively. c Protein abundance and mRNA expression changes were compared for the co-regulated paralogs. Transcriptional regulation was inferred when both protein and mRNA were significantly regulated with a consistent fold change at the same time point (see Methods for details). Protein and mRNA profiles are shown for two representative cases