Identification of widely expressed genes with CNS specific regulation of AS. Microarray profiled genes with single or multiple alternative exons displaying differential alternative splicing (AS) in the central nervous system (CNS) were identified using statistical procedures that control for covariation in transcript levels (see Results and Materials and methods). (a) The top 100 genes with the most significant CNS associated AS levels are hierarchically clustered on both axes, based on their overall AS level similarity across 27 profiled tissues. (b) The corresponding transcript levels of the same genes, displayed in the same order. Color scales representing AS levels (percentage exon exclusion) and transcript levels (z-score scale) are shown below each panel. The z-score represents the number of standard deviations from the mean transcript level (center of the scale, in black) of the given event. Increasingly bright yellow represents lower transcript levels, and increasingly bright blue represents higher transcript levels. White rectangles in the AS clustergram indicate removed GenASAP (Generative Model for the Alternative Splicing Array Platform) values. These values were removed when transcript levels from the same genes (as measured using probes specific for constitutive exons on the microarray) were below the 95th percentile of the negative control probes.