(SAGE) to analyze the temporal response of human pulmonary artery endothelial cells (HPAECs) to short-term chronic hypoxia at the level of transcription. Primary cultures of HPAECs were exposed to 1% O2 hypoxia for 8 and 24 h and compared with identical same-passage cells cultured under standard (5% CO2-95% air) conditions. Hierarchical clustering of significant hypoxia-responsive genes identified temporal changes in the expressions of a number of well-described gene families including those encoding proteins involved in thrombosis, stress response, apoptosis, angiogenesis, and cell proliferation. These experiments build on previously published data describing the transcriptomic response of human aortic endothelial cells (HAECs) obtained from the same donor and cultured under identical conditions, and we have thus taken advantage of the immortality of SAGE data to make direct comparisons between these two data sets. This approach revealed comprehensive information relating to the similarities and differences at the level of mRNA expression between HAECs and HPAECs. For example, we found differences in the cell type-specific response to hypoxia among genes encoding cytoskeletal factors, including paxillin, and proteins involved in metabolic energy production, the response to oxidative stress, and vasoreactivity (e.g., endothelin-1). These efforts contribute to the expanding collection of publicly available SAGE data and provide a foundation on which to base further efforts to understand the characteristics of the vascular response to hypoxia in the pulmonary circulation relative to systemic vasculature.transcriptome; temporal; serial analysis of gene expression HYPOXIA is an important pathological stimulus that has profound effects on the vasculature. These include alteration of vascular tone, coagulant function, redox homeostasis, endothelial permeability, and cell proliferation. Significantly, the response to hypoxia is different in distinct vascular beds. Hypoxia elicits systemic vasodilation, yet causes acute pulmonary vasoconstriction, which, if sustained, leads to profound remodeling of the pulmonary vasculature and culminates in structural-based increases in pulmonary vascular resistance and the subsequent development of pulmonary hypertension (30,33,36).Although the focus of intense research for nearly a century, the mechanisms underlying these differential vascular responses to hypoxia remain unclear (55). It has, however, been previously noted that fundamental molecular differences exist between the response of pulmonary and systemic vascular cells to hypoxia (19), but little information exists regarding the differences in the genome-wide response to hypoxic stress between pulmonary and systemic vascular endothelial cells.Despite the intense interest in the cellular response to hypoxia, particularly in the context of vascular biology, there have been few systematic attempts to document the transcriptional response to hypoxia in primary vascular endothelial cells. We (40) previously utilized serial ana...