Figure 2

Statistical analysis of SILAC data of two patient cells. (A) Upper panels, log2 distributions of Medium (M)/Light (L) and Heavy (H)/Light (L) ratios of proteins quantified in SILAC analysis. Dashed lines represented log2 transformed cut-off values (>1.5, <0.67). Lower panel, statistical summary of ratios of two patient cells. (B) Ratios of various housekeeping proteins identified in SILAC analysis. (C) Scatter plot of log2 transformed patient cells/control cells ratios. X- and Y- axes represent log2 transformed M/L and H/L ratios, respectively, as indicated in the graph. (D) Upper panels, Venn diagrams show the number of overlapping altered proteins between the two patient cells. Lower panel, if there were only two quantified peptides, individual peptides must have met the cut-off value (>1.5 or <0.67) and proteins found not to meet this criteria were discarded. “Manual check-passed” represents remaining proteins after implementing the above criteria. (E) Summary of quantitative proteomics.