A database for regional gene expression in the human brain

Alterations in gene expression levels have been widely studied for various neurological diseases, but few studies have sought to characterize genome-wide gene expression patterns from various regions of the normal brain. A sensitive method for quantifying transcript levels, Serial Analysis of Gene Expression (SAGE), was used to assay expression levels in white matter, thalamus, and cerebellum from the same normal brain, obtained by rapid autopsy. The complete dataset for these SAGE libraries are posted on the Cancer Genome Anatomy Project sponsored SAGEmap website where library comparisons can be made, or the data downloaded for local analysis. The expression of several region-specific genes--neurogenic differentiation 1 (cerebellum), cocaine- and amphetamine-regulated transcript (thalamus), and neurogranin (white matter)--was confirmed using quantitative fluorescent real-time RT-PCR. Further informatics analysis of the data yielded a list of brain-specific genes. The database formed by this analysis provides a means to investigate the expression status of genes involved in the region specific functions of the normal brain. These normal brain gene expression levels also are useful for comparison to pathological expression levels and a sensitive means to determine gene expression in a normal adult brain prior to formulating therapeutic strategies.