Oxidized phospholipids are thought to promote atherogenesis by stimulating endothelial cells (ECs) to produce inflammatory cytokines, such as IL-8. In studies with mouse models, we previously demonstrated that genetic variation in inflammatory responses of endothelial cells to oxidized lipids contributes importantly to atherosclerosis susceptibility. We now show that similar variations occur in cultured aortic ECs derived from multiple heart transplant donors. These variations were stably maintained between passages and, thus, reflect either genetic or epigenetic regulatory differences. Expression array analysis of aortic EC cultures derived from 12 individuals revealed that >1,000 genes were regulated by oxidized phospholipids. We have used the observed variations in the sampled population to construct a gene coexpression network comprised of 15 modules of highly connected genes. We show that several identified modules are significantly enriched in genes for known pathways and confirm a module enriched for unfolded protein response (UPR) genes using siRNA and the UPR inducer tunicamycin. On the basis of the constructed network, we predicted that a gene of unknown function (MGC4504) present in the UPR module is a target for UPR transcriptional activator ATF4. Our data also indicate that IL-8 is present in the UPR module and is regulated, in part, by the UPR. We validate these by using siRNA. In conclusion, we show that interindividual variability can be used to group genes into pathways and predict gene-gene regulatory relationships, thus identifying targets potentially involved in susceptibility to common diseases such as atherosclerosis.genetic ͉ interleukin 8 ͉ atherosclerosis ͉ unfolded protein response ͉ network A therosclerosis, the major cause of heart disease, is characterized by the accumulation of cholesterol, inflammatory cells, smooth muscle cells, and fibrous elements beneath the endothelial cell (EC) monolayer that lines the artery wall (1). Although numerous risk factors for atherosclerosis, such as elevated blood pressure, hypercholesterolemia, and smoking, have been recognized, these factors do not alone account for the genetic contribution to risk (2). An important mechanism contributing to the recruitment of inflammatory cells in atherosclerosis is the induction of adhesion molecules, growth factors, and cytokines in vascular ECs by oxidized phospholipids, such as oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycero-phosphorylcholine (oxPAPC) derived from lipoproteins trapped in the vessel wall (3).We have previously demonstrated that ECs from different strains of mice show differences in the induction of inflammatory genes when treated with oxidized lipoproteins, and that these differences segregate with susceptibility to atherosclerosis (4, 5). Studies in human populations show significant variability in the plasma levels of inflammatory mediators associated with atherosclerosis, including IL-8 and C-reactive protein (6-8). The plasma levels of cytokines are influenced by genetic and environmenta...