PMC

Notations are similar to . upper left: x axis: PCor of X_·1 and X \ (X_·1, X_·2), y axis: X_·2 and X \ (X_·1, X_·2) (CCor_1,2, similarity within first module); upper right: x axis: PCor of X_·1 and X \ (X_·1, X_·p1+1), y axis: X_·p1+1 and X \ (X_·1, X_·p1+1) (CCor_1,p1+1, similarity between first and second module); lower left: x axis: PCor of X_·p1+p2+1 and X \ (X_·p1+p2+1, X_·p1+p2+2), y axis: X_·p1+p2+2 and X \ (X_·p1+p2+1, X_·p1+p2+2) (CCor_{p1+p2+1,p1+p2+2}, similarity within third module); lower right: x axis: PCor of X_·1 and X \ (X_·1, X_·p1+p2+1), y axis: X_·p1+p2+1 and X \ (X_·1, X_·p1+p2+1) (CCor_1,p1+p2+1, similarity between first and third module);

p₁ = p₂ = 100 and n = 100. Within-module and between-module similarities correspond to CCor_1,2 and CCor_1,p1+1. Points in plots represent the empirical estimates by taking mean of CCor calculated from 100 simulated datasets with error bars representing the standard deviation of the 100 estimates.

upper left: observations of two genes from same module; upper right: observations of two genes from different modules; lower left: x axis: Pearson correlation coefficients of X_·1 and X \ (X_·1, X_·2) (all the genes except genes 1 and 2), y axis: X_·2 and X \ (X_·1, X_·2); lower right: x axis: Pearson correlation coefficients of X_·1 and X \ (X_·1, X_·p1+1) (all the genes except genes 1 and p₁ + 1), y axis: X_·p1+1 and X \ (X_·1, X_·p1+1)

5 best GO enrichment p values from all modules identified using each similarity measures are log transformed. Bar plots show the mean of these pooled p values and error bars stand for 95% confidence intervals. P values shown on top of the panels are obtained by applying Fisher’s method on pairwise comparison p values of mCCor vs other three methods.