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. 2013 Apr 25;9(4):e1003455. doi: 10.1371/journal.pgen.1003455

Figure 1. Stratified Q–Q plot and Stratified True Discovery Rate plots.

Figure 1

Upper panel: Stratified Q-Q plot of nominal versus empirical −log10 p-values (corrected for inflation) in A) schizophrenia (SCZ) below the standard GWAS threshold of p<5×10−8 as a function of significance of the association with bipolar disorder (BD) at the level of −log10(p)>0, −log10(p)>1, −log10(p)>2, −log10(p)>3 corresponding to p<1, p<0.1, p<0.01, p<0.001, respectively, and in B) BD below the standard GWAS threshold of p<5×10−8 as a function of significance of association with SCZ at the level of −log10(p)>0, −log10(p)>1, −log10(p)>2, −log10(p)>3 corresponding to p<1, p<0.1, p<0.01, p<0.001, respectively. Dotted lines indicate the null-hypothesis. Lower panel: Stratified True Discovery Rate (TDR) plots illustrating the increase in TDR associated with increased pleiotropic enrichment in C) SCZ conditional on nominal BD p-values (SCZ|BD), and D) BD conditional on nominal SCZ p-values (BD|SCZ). For more information about QQ plots, see Text S1.