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Table 1 Significantly differentially methylated CpG probes identified in AMD RPE cells

From: Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes

Probe ID Log2 FC Adjusted p value False discovery rate (< 0.2) Δβ (* > 10%) Chromosome Position Relation to CpG island UCSC gene name Relation to gene
cg18486102 1.81 1.08E−12 4.6E−07 *0.20 chr12 50297777 Island FAIM2 TSS200
cg18934822 − 3.00 1.18E−09 2.5E−04 *− 0.11 chr1 2191402 Open Sea SKI Body
cg23169512 − 3.51 2.08E−08 2.9E−03 *− 0.33 chr15 60290666 N_Shore   
cg22508626 1.02 7.03E−07 6.0E−02 *0.12 chr6 30879905 N_Shore GTF2H4 Body
cg01560972 − 3.87 2.03E−06 1.4E−01 *− 0.33 chr11 8190837 S_Shore RIC3 TSS1500
cg26962595 1.18 2.75E−06 1.6E−01 0.02 chr11 72504889 Island STARD10 TSS200
cg11897517 1.67 3.87E−06 1.6E−01 0.02 chr6 109761938 Island SMPD2 5′UTR
cg04838987 − 1.76 3.98E−06 1.6E−01 *− 0.18 chr20 33734406 N_Shore EDEM2 Body
cg11241206 − 2.82 4.44E−06 1.6E−01 *− 0.35 chr11 27723128 S_Shore BDNF TSS1500; 5′UTR
cg03611060 2.51 5.00E−06 1.6E−01 *− 0.14 chr1 59281067 Island   
cg26347887 − 2.87 5.16E−06 1.6E−01 *− 0.28 chr2 88927196 Island EIF2AK3 TSS200
  1. Δβ mean β value AMD—mean β value control, TSS transcription start site, 5′UTR 5-untranslated region, 3′-UTR 3-untranslated region, Body gene body, Intragenic intragenic region
  2. Analysis of Illumina 450k BeadChip array data using linear interaction modeling considering independent variables (sex M/F and batch effect) and their interaction with DNA methylation. Significantly differentially methylated CpG probes in contrasts AMD/normal with a FDR of < 20% are shown. cg23169512 is approximately 10 kb from FOXB1, and cg03611061 is within the long intergenic non-protein coding RNA 1135 and 30 kb upstream of JUN proto-oncogene