The correlation between the mRNA difference at 0 and 72 hours and the corresponding protein difference.

Correlation between RNA expression level differences, ΔR ≡  RNA(t = 72) − RNA(t = 0), and protein level differences ΔP ≡ P(t = 72) − P(t = 0). Expression levels of proteins that have more than one conformation were summed. In this regression analysis we retained only RNA probe sets that correspond to single genes (the remaining probe sets lacked the ambiguity of multiple probe sets per Locus Link) and that had a “present” Affymetrix indicator and an amplitude more than 20 both at t = 0 and t = 72 hours. There were 51 different proteins that satisfy these conditions. The linear association r between changes in RNA levels (ΔR) and changes in protein levels (ΔP) of the remaining 51 genes is only 0.58, where r is the Pearson correlation coefficient defined as r(ΔP,ΔR) = ∑_i (ΔP_i −$ΔP̄)$(ΔR_i−$ΔR̄)$/$∑i (ΔPi−ΔP̄)2 ∑i (ΔRi−ΔR̄)2.$However, about 80% of the genes are located in the first and third quadrants, indicating a general trend that genes with increasing/decreasing levels of RNA also have increasing/decreasing protein levels.