Computational exploration of the human cardiovascular genome and its application to understanding human fetal heart development

A human cardiovascular gene expression database was established as a resource to aid in answering questions regarding cardiovascular biology. The large-scale generation of expressed sequence tags (ESTs) from several human cardiovascular-based cDNA libraries was the method chosen, as it is an efficient means for gene discovery. Approximately 54,000 ESTs were generated from several human heart and aorta cDNA libraries in our laboratory; and have been combined with ∼57,000 cardiovascular-based ESTs retrieved from the public databases to form a comprehensive gene expression database.; This database was employed along with cDNA microarray hybridization, to estimate the total number of genes expressed in the cardiovascular system (CVS). The estimated 21,000 to 27,000 genes expressed in the CVS form the cardiovascular genome [further refined to a lower estimate of 20,498 ± 1,368 and an upper estimate of 24,913 ± 3,459 unique expressed genes]; which can be defined as the complete spectrum of genes expressed in the CVS. Extending this concept toward defining the physical genome of the CVS led to the identification of two regions with higher, and one with a lower, density of genes on chromosomes 21 and 22 than was expected by chance alone [using an additional statistical method, the clusters were refined to four regions with a higher, and two with a lower, density of genes on chromosomes 21 and 22].; Our current 10,000+ element cDNA CardioChip microarray was also used to compile an index of genes preferentially expressed in the human fetal or adult hearts. This resulted in the identification of 1,255 candidate differentially expressed genes, the majority of which were previously unknown. Functional categorization of the known differentially expressed genes revealed some striking differences between the fetal and adult hearts.; The generation of our cardiovascular gene index has provided us with a powerful tool to perform many analyses to help answer questions regarding cardiovascular biology. The continued exploitation of this resource, as both a gene expression index and a cDNA microarray, will undoubtedly remain an important resource for years to come.