If a particular SNP is cis- or trans-acting on multiple genes, it is plausible that those genes are biologically related. Co-expression between these genes provides circumstantial evidence this is the case, strengthening the likelihood such cis- and trans-eQTLs are real. We assessed this in the peripheral blood data, by using the expression data of the 1,240 samples, run on the comprehensive HT12 expression platform. As we had removed 25 PCs (to remove physiological, environmental variation, and systematic experimental variation) for the trans-eQTL analyses, we decided to confine co-expression analyses to this expression dataset. As there are 43,202 HT12 probes that we mapped to a known genomic location, 43,202×43,201/2 = 933,184,801 probe-pairs exist. Given 1,240 samples, a Pearson correlation coefficient r≥0.19 corresponds to a p<0.05 when applying stringent Bonferroni correction for these number of probe-pairs.
