Although congenital heart malformations are the most common birth defects in humans, the underlying pathomechanisms remain widely unknown. Through linkage analyzes and candidate-gene approaches, several gene mutations causing congenital heart defects (e.g., CITED2, GATA4, NKX2-5) have been identified. However, most heart malformations display variable expressivity and penetrance, which indicates a multifactorial and multigenic basis. This suggests that the regulatory context of transcription factors plays an important role in the manifestation of the defects. In order to better understand the molecular pathways in cardiogenesis and disease we studied the global genetic network that is deregulated in malformed hearts more