Raw gene expression two-color microarray intensity data (available at GSE30272) were loess-normalized as previously described1. Probes were re-annotated to the hg19 genome using the Gemma tool52 leaving 31,699 gene expression probes on 249 samples that had both Illumina 450k DNAm and expression data. Differential expression analysis comparing pre- and post-natal expression levels was performed using limma46. We annotated each 450k probe to its nearest gene in the expression data by distance, and computed the Pearson correlation between proportion DNAm and gene expression level, and converted these correlations to Z-scores and corresponding p-values (e.g. Z~ρ(1−ρ)2/(N−1)). For the DMR-expression analysis, we matched each DMR to all probes corresponding to the nearest gene, and retained the most correlated DMR-probe correlation. For block-expression analysis, we identified which probes, and their evidence for differential expression, were present in each block using genomic coordinates.
