Fig. 7

Identification of genes whose RNA expressions are most closely associated with DNA methylation in promoters (a–f) and gene bodies (g–l). a TINAG, b NXPE4, c PAK1, d CNGA1, e SAMD13, f LINC02038, g ESRP2, h HOXB2, i REP15, j GPX2, k LINC02038 and l MIR194-2HG. We plotted promoter methylation rate against log2 normalized gene expression. The genes were selected based on the following criteria: (1) their p values of the empirical Bayes t test (using R package limma) of logit-transformed promoter methylation between NEC and control colons ≤ 0.05; (2) the difference in logit-transformed promoter methylation between NEC and control colons ≥ 1; (3), the adjusted p values of the t test for Pearson’s correlation between gene expression and promoter methylation ≤ 0.1; and (4) those with adjusted p values ≤ 0.05