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Table 3 Differentially methylated CpGs

From: DNA methylation in cord blood in association with prenatal depressive symptoms

Group 1 Group 2 Gene Location Probe Log2 fold change Mean SD Adjusted p-value Regulatory feature
Anxiety and prenatal depressive symptoms Healthy control ATP Binding Cassette Subfamily F Member 1(ABCF1) chr6. 30539063 cg05385119 − 0.21 − 3.80 (0.35), − 3,60(0,26) 0.037 Promoter Associated
   Located upstream of Homo sapiens integrator complex subunit 10 gene (INTS10) chr8. 19711803 cg00017362 0.18 3.04(0,29), 2,89(0.26) 0.037  
Healthy controls Prenatal depressive symptoms with SSRI Nuclear Factor I A (NFIA) chr1. 61549982 cg18946602 − 0.91 2.05(0.50), 2.82 (0.96) 0.005  
   Chromosome 2 open reading frame 40 (C2orf40) chr2 106682209 cg17161250 − 0.71 − 3.83(0.38), − 3.14(1.10) 0.004 Unclassified cell-type specific
   Immunoglobulin Superfamily Member 11 (IGSF11) chr3 118864895 cg20675391 − 0.70 3.74(0.43), 4.35(1.11) 0.024 Unclassified
   Cereblon (CRBN) chr3 3221595 cg20787969 − 0.57 − 4.39(0.26), − 3.83(1.39) 0.020 Promoter Associated
   Cyclin-Dependent Kinase 11B (CDK11B) chr1 1655867 cg00669623 − 0.29 − 3.32 (0.12), − 3.04(0.74) 0.021 Promoter Associated
   WD Repeat Containing. Antisense To TP73 (WRAP73) chr1 3551807 cg04386615 − 0.54 3.64(0.37), 4.15(0.46) 0.048  
   G Protein-Coupled Receptor Kinase 4 (GRK4) chr4 3033304 cg03178823 0.43 2.47(0.20), 1.99(0.93) 0.010  
   MyoD Family Inhibitor Domain Containing (MDFIC) chr7 114562316 cg02239805 0.44 − 1.52(0.09), − 1.96(1.42) 0.010 Promoter Associated
   Potassium Voltage-Gated Channel Modifier Subfamily S Member 2 (KCNS2) chr8 99441950 cg02143496 0.49 3.19(0.29), 2.71(0.88) 0.010  
   LRRN4 C-Terminal Like (LRRN4CL) chr11 62455369 cg03353995 0.49 − 2,38(0.32), − 2,80(0.33) 0.041  
   Mitogen-Activated Protein Kinase Kinase Kinase Kinase 5 (MAP4K5) chr14 50999680 cg21062897 0.49 − 0.85 (0.15),—1.33(1.61) 0.018 Promoter Associated
    chr3 169476270 cg16056894 0.56 − 1.33(0.35), − 1.82(0.67) 0.029  
   SOX2 Overlapping Transcript (SOX2OT) chr3 181444989 cg17202313 0.57 − 3.76(0.36), − 4.24(0.70) 0.030 Unclassified cell-type specific
   Chromosome 10 open reading frame 11 (C10orf11) chr10 77871958 cg24280832 0.98 1.54(0.39), 0.51(1.72)  < 0.000  
   Nuclear Factor I A (NFIA) chr1 61549982 cg18946602 − 0.80 2.11(0.56), 2.82(0.95) 0.041  
Prenatal depressive symptoms without SSRI Prenatal depressive symptoms with SSRI Chromosome 2 open reading frame 40 (C2orf40) chr2 106682209 cg17161250 − 0.72 − 3.87(0.41), − 3.14(1.10) 0.003 Unclassified cell-type specific
   Cereblon (CRBN) chr3 3221595 cg20787969 − 0.57 − 4.38(0.25), − 3.83(1.39) 0.026 Promoter Associated
   Primary Ciliary Dyskinesia Protein 1 (PCDP1) chr2 120301847 cg23747904 − 0.55 − 4.17(0.27), − 3.67(1.37) 0.040  
   WD Repeat Containing. Antisense To TP73 (WRAP73) chr1 3551807 cg04386615 − 0.54 3.66(0.33), 4.15(0.46) 0.040  
    chr1 1712021 cg23678594 − 0.34 − 4.31(0.19), − 3.98(0.43) 0.038 Promoter Associated
   Cyclin-Dependent Kinase 11B (CDK11B) chr1 1655867 cg00669623 − 0.29 − 3.32(0.13), − 3.05(0.73) 0.037 Promoter Associated
   Solute Carrier Family 16 Member 11 (SLC16A11) chr17 6947200 cg15639045 − 0.28 − 3.54(0.14), − 3.26(0.49) 0.011  
   Uncharacterized LOC284930 chr22 48182596 cg00331486 0.36 1.69(0.23), 1.35(0.59) 0.043  
   MyoD Family Inhibitor Domain Containing (MDFIC) chr7 114562316 cg02239805 0.45 − 1.51(0.08), 1.96(1.42) 0.007 Promoter Associated
   G Protein-Coupled Receptor Kinase 4 (GRK4) chr4 3033304 cg03178823 0.45 2.47(0.21), 1.99(0.93) 0.004  
   Mitogen-Activated Protein Kinase Kinase Kinase Kinase 5 (MAP4K5) chr14 50999680 cg21062897 0.48 − 0.90(0.15), − 1.33(1.61) 0.036 Promoter Associated
    chr3 169476270 cg16056894 0.56 − 1.33(0.36), − 1.82(0.67) 0.038  
   Chromosome 10 open reading frame 11 (C10orf11) chr10 77871958 cg24280832 0.94 1.48(0.39), 0.51(1.72)  < 0.000  
  1. Location: chromosome and genomic position. Group difference in DNA methylation in specific CpGs are presented as log2 fold change (log2 (M-value group1/M-value group 2)) between the groups, meaning that a negative log2 fold changes means lower DNA methylation in group 1. Mean SD = mean standard deviation for group 1, group 2
  2. chromosome (chr), standard deviation (SD)