Gene expression profiles were generated using RNA obtained by TRIzol extraction (Invitrogen) from microdissected alternate sections of the same 59 EDRN lung AD/NTL frozen tissue pairs used for the DNA methylation analysis. Expression data were obtained using the Illumina Human WG-6 v3.0 Expression BeadChips (Illumina) at the Genomics Core at UT Southwestern. Bead-summarized data were obtained using the Illumina BeadStudio software, expression values were log2-transformed, and Robust Spline Normalization (RSN) was performed with the lumi package in R (Du et al. 2008 (link)). The ReMOAT annotation of gene expression data was used to include only “perfect” and “good” annotated probes (Barbosa-Morais et al. 2010 (link)). Exploratory quality-control analyses revealed no strong batch effects (data not shown), although one tumor sample was excluded (3035_T) due to quality concerns. Out of 766 differentially methylated genes identified (Q < 0.05, median β-value difference ≥0.2), we were able to examine gene expression levels for 709 genes after the probe quality filtering detailed above. For genes with multiple probes, we selected the probe with the highest variance and analyzed differential expression using t-tests and a Benjamini-Hochberg (BH) multiple comparisons correction. Statistical significance was called at BH-adjusted p < 0.05. An additional stringent filter of mean twofold change was used to identify top changing genes. Correlation between gene expression and DNA methylation for each gene was measured using the Spearman correlation coefficient. For genes with multiple probes measuring DNA methylation, we selected the probe with the highest SD/SDmax value for DNA methylation.