Blood vessel growth by angiogenesis plays an essential role in embryonic development, wound healing, and tumor growth. To understand the molecular cues underlying this process we have used the PCR-based subtractive hybridization method, representational difference analysis, to identify genes upregulated in endothelial cells (EC) forming tubes in 3D collagen gels, compared to migrating and proliferating cells in 2D cultures. We identified several previously characterized angiogenic markers, including the alpha(v) chain of the alpha(v)beta3 integrin and plasminogen activator inhibitor-1, suggesting overlap in gene expression between tube-forming cells in vitro and in vivo. We also found a 2- to 10-fold upregulation of (beta)ig-h3 (a collagen-binding extracellular matrix protein), NrCAM (a "neural" cell adhesion molecule), Annexin II (a tPA receptor), ESM-1 (an EC-specific molecule of unknown function), and Id2 (an inhibitory bHLH transcription factor). We identified a novel splice variant of the ESM-1 gene and also detected dramatically enhanced expression of ESM-1 and (beta)ig-h3 in several tumors. Antisense oligonucleotides to (beta)ig-h3 blocked both gene expression and tube formation in vitro, suggesting that (beta)ig-h3 may play a critical role in EC-matrix interactions. These data expand the suite of genes implicated in vascular remodeling and angiogenesis.