Correlation of the positive probe and exon density maps [5%false positive (FP) rate][S5 (6)] for chromosomes 21 (A) and 22 (B). For each map, the lowest graph depicts the positive probe density present in 57-kb bins (average genomic size for genes on chromosome 21 (11). Above this plot is the density of nucleotides located within exons present in each bin. The graph overlaying a cartoon of each chromosome is the local correlation coefficient of the exon density and the positive probe density calculated over a 5.7-Mb window. A correlation coefficient is not calculated in regions where the percentage of positive exon density falls below 25% over the 5.7-Mb window. Thus, the chromosome 21 region near the centromere that is relatively sparse in exon annotations is not analyzed for correlation with positive probe density given the relative lack of variation in the exon density. Above the positive probe density maps are the experimentally verified regions (downward arrows). The DGCR region of chromosome 22 is boxed in (B).

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