Figure 4c provides an example for Ubiquitin (UBA52), for which a strong cis-eQTL was observed for probe GI_15451941 with rs2314664 (Spearman's correlation coefficient P-Value = 1.11 × 10-16) in the HapMap B cell line dataset. Within this probe three other polymorphism map (rs6554, rs34040670 and rs3209501), of which rs6554 is in near perfect LD with rs2314664 (r2 = 0.98, HapMap CEU population), suggesting this cis-eQTL does not reflect a real expression difference, but rather a difference in hybridization efficacy. Co-expression with other genes is already present in an unconditioned co-expression analysis, because the distribution of co-expression for UBA52 with all other genes differs significantly from a theoretical null-distribution (Wilcoxon-Mann Whitney P-Value < 1 × 10-12). However, in the conditioned co-expression analysis, this difference is more pronounced (see figure 4c). When confining this analysis to a set of 156 known interactions for UBA52, overall co-expression was significantly stronger for these pairs of genes in the conditioned (mean absolute Spearman's correlation coefficient = 0.39) than in the unconditioned co-expression analysis (mean absolute Spearman's correlation coefficient = 0.20, Wilcoxon-Mann Whitney P-Value < 10-50).
