As a further method of validating our microarrays, we compared our average observed levels of transcriptional and epigenetic signals to previously described signals within specific gene elements across the entire locus profiled. To do so, we examined the absolute levels of transcription, histone acetylation and DNA methylation for all subjects combined (Fig. S3), and compared them to previously published relationships between levels of gene expression, DNA methylation, and histone acetylation across 5′ regulatory regions, exons, and introns. First, previous studies have indicated that much of the genome is actively transcribed [22] but that levels of transcription are generally higher within annotated exons relative to other regions. As expected, inside exons we observed significantly higher transcription than the overall levels of transcription throughout all regions in the locus (P = 1.47×10−155 by Student's T-test, P = 0 by Wilcoxon Rank Sum test). In contrast, we observed levels of transcription just upstream of genes (−1800 bp to transcription start site) and in intronic regions that were indistinguishable from the baseline. These data indicate that the signals observed by our microarray accurately detect
