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Table 3 Differentially methylated, hydroxymethylated, and unmodified regions in the middle temporal gyrus

From: Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood

GenePositionGene featurenp valueŠidák PAverage Δ% (range Δ%)
5mC      
OXTchr20:3051954-3052484TSS; Intron; 5′UTR; CDS10 (0 up; 10 down)1.43E−091.07E−06− 3.76 (− 6.94:− 0.43)
5hmC
CHRNB1chr17:7348322-7348439TSS; Exon; 5′UTR5 (5 up; 0 down)2.63E−074.01E−041.46 (0.70:1.96)
UC
ACTR3C; LRRC61chr7:150019955-150020946TSS; Intron; Exon; 5′UTR17 (1 up; 16 down)3.54E−121.42E−09− 0.57 (− 1.34:0.02)
RHBDF2chr17:74475240-74475403Intron; CDS5 (0 up; 5 down)1.99E−094.85E−06− 3.45 (− 4.71:− 1.42)
TMC8chr17:76128522-76128907Intron; CDS8 (0 up; 8 down)3.29E−093.39E−06− 1.26 (− 2.84:− 0.26)
ASPGchr14:104551867-104552210TSS; Intron; 5′UTR; CDS5 (0 up; 5 down)1.00E−081.16E−05− 1.21 (− 2.49:− 0.28)
PIEZO1chr16:88844969-88845205Intron3 (0 up; 3 down)1.87E−073.14E−04− 3.08 (− 3.76:− 2.32)
VWA7chr6:31734106-31734472Intron; CDS10 (10 up; 0 down)2.04E−072.21E−043.39 (2.24:4.23)
CLMAT3; SPARCchr5:151066460-151066731Exon; TSS; 5′UTR6 (0 up; 6 down)5.21E−077.62E−04− 0.29 (− 0.64:0.21)
KIAA1522chr1:33231070-33231314TSS; Exon; 5′UTR; Intron6 (0 up; 6 down)8.48E−071.38E−03− 1.85 (− 2.43:− 1.3)
C3chr19:6713227-6713460Intron; CDS3 (1 up; 2 down)9.21E−071.57E−03− 1.20 (− 2.1:0.46)
PRSS22chr16:2908157-2908246TSS; Exon; 5′UTR4 (0 up; 4 down)1.02E−064.52E−03− 1.56 (− 1.91:− 1.39)
FRAT1chr10:99080756-99081017Exon3 (3 up; 0 down)1.50E−062.28E−032.34 (1.57:3.03)
  1. Differentially methylated (5mC), hydroxymethylated (5hmC), and unmodified (UC) regions in a comparison of Alzheimer’s disease patients (n = 45) and controls (n = 35). Displayed for each region is the UCSC gene name, chromosomal position (genome build 37), gene feature (TSS, transcription start site; 5′UTR, 5′ untranslated region; CDS, coding sequence), number of probes in region and number of upregulated and downregulated probes (n), p value and multiple testing-corrected p (Šidák-P), and average change in beta value (Alzheimer’s disease - control), including the range of the probe differences