Note that the three genes flanking either side of the deleted region were not differentially expressed (Fig. 1b). In fact, of the 311 genes on chromosome 22 that were outside of 22q11.2 and had a mean >1 FPKM in either the control or patient groups, 169 were expressed at a higher level in the patient samples; 142 were lower. Of these, only 14 genes showed a significant difference between patients and controls at p < 0.05 (7 were decreased in patients; 7 increased). The difference between significantly down-regulated genes on 22q11.2 compared with the number of significantly differentially expressed genes on the rest of chromosome 22 was highly significant (χ2 test p-value < 2.2e-16).
