Vascular endothelium (EC) plays a central role in many processes such
as inflammation, angiogenesis, and the development of vascular
diseases.  As a step toward a better understanding of EC biology, 
we set out to characterize the gene expression profile of EC both 
in vitro and in vivo by utilizing a whole-genome approach.  We first
undertook a high-throughput sequencing project on multiple EC 
libraries to obtain the entire repertoire of EC expressed genes.
These were then represented on high-density custom-designed 
oligonucleotide microarrays, together with most of the non-redundant 
human genes (~50,000-elements, representing ~32,000 independent
genes).  Large-scale transcriptional profiling was then performed 
to compare the gene expression profiles of variously stimulated EC
and multiple non-EC human cells.  These analyses revealed that EC
express roughly 6,600 genes with 380 of these found only in this
cell type.  The majority of the EC-enriched genes appear novel or 
largely uncharacterized.  Additionally, many of the EC-enriched
genes demonstrate distinct patterns of expression when 
systematically profiled across a panel of major tissues, revealing
the heterogeneity of EC in vivo.  In summary, using genome-scale 
gene expression profiling of most of the expressed human genes, we 
have defined the molecular map of human vascular endothelium both 
in vitro and in vivo. These analyses highlight the complexity and
diversity of the EC transcriptome.