Table 1. Significant associations between methylation and BDI II score.

Method	Probes	Probes with gene annotation	No. of genes	Genes with more than one significant probe (no. of probes)
Limma	24	24	23	TACC3 (2)
Limma pairwise	474	474	445	Up: MYO16-AS1 (2),SCAND3 (2),CRYAA (2),PSMA8 (2),MIR153-2 (2),PAK3 (2),SIDT1 (2),SLC2A2 (2),TAF4B (2),TBX3 (2),SLC30A4 (2) Down: LOC100505545 (2),UBE2F (2),AGT (2),NTSR2 (2),GATA4 (2),CD82 (2),LOC401177 (2),MIR346 (2),MSX2 (2),MBIP (2),TPM1 (2),PPT2 (2)
MethyAnalysis	491	491	351	Up: SLC2A2 (6),MYO7A (5),HIST1H4F (5),HPS3 (5),SPACA7 (4),ZNF419 (3),CAHM (2),LINC00439 (2),KDELR3 (2),WFDC12 (2),RNF183 (2),ABCB7 (2),TXLNG2P (2),TMEM9 (2),LOC283914 (2),BCORP1 (2),MAF (2),MDM4 (2),STRA6 (2),ZNF205 (2),AFAP1-AS1 (2),MYOM2 (2) Down: COL9A2 (7),LOC100505545 (5),LRRC32 (5),PABPN1L (5),LGALS8 (5),LGI1 (5),PITPNA-AS1 (4),NTSR2 (4),CD82 (4),LOC100507254 (3),FOXP4 (3),PAOX (3),CADM1 (3),LOC253044 (3),TSKU (3),C17orf78 (3),MIR183 (3),OR1F1 (3),LGI2 (3),PLEKHG5 (3),TP73 (3),PRR3 (3),SLC25A12 (3),MIR3661 (2),PLK3 (2),C1orf172 (2),TMEM198 (2),EVC2 (2),CSHL1 (2),LACE1 (2),PRPF40B (2),SNORD41 (2),GPR20 (2),HOXA13 (2),VSX2 (2),APOC1 (2),INHBB (2),DRAXIN (2),LOC401177 (2),MCAM (2),MSX2 (2),C8orf22 (2),MRTO4 (2),RXFP3 (2),TBC1D8B (2),PURA (2),SGSH (2),TBX5 (2),TNXB (2),TPM1 (2),VEZF1 (2),FOXQ1 (2)

Summary of significant (<0.05) methylation-phenotype associations between individuals with minimal depressive symptomatology (a score of 1–13) and those with mild depression (a score of 14–25) on the Beck Depression Inventory II (BDI II). As well as P<0.05 for a probe to be significant, each variable was removed if at least one probe did not pass a Bonferroni-corrected P-value threshold. With 149 variables queried, this threshold was 0.05/149=0.00033.