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Table 3 Methylation of microRNAs and their target genes

From: Childhood abuse is associated with methylation of multiple loci in adult DNA

MicroRNA Number of targets Number hypo-methylated Number hyper-methylated Hypomethylated targets Enrichment p-value MicroRNA methylation
mir-514 49 10 1 AFF4, BAALC, BRWD1, CARM1, ENAH, KLF13, MYO1B, NR3C1, SVIL, TCF12 5.71E-05 hypermethylated
let-7d 320 26 6 ATP2A2, BACH1, BRWD1, CDV3, CHD4, CPSF4, DCUN1D2, DOCK3, DOT1L, EFHD2, EZH2, GGA3, LIMD2, LRIG1, MECP2, MGAT4A, MIB1, MLL5, PARD6B, PBX3, PRTG, PTPRU, RDH10, SOCS1, UNC5A, WDR37 0.0030 hypermethylated
mir-520c 274 23 3 ASF1B, BCL2L11, BRP44L, DDHD1, DPYSL5, FLT1, FNDC3B, INHBB, KCNMA1, KLF13, MAP3K14, MECP2, MKNK2, MTUS1, ORMDL3, PBX3, PFN2, RGL1, SMAD2, UBE2Q2, WDR37, ZFP36L2, ZFPM2 0.0035 hypermethylated
mir-215 37 6 0 ARFGEF1, FNDC3B, GRHL1, KLHDC5, LRRFIP1, MECP2 0.0060 hypermethylated
mir-519a 377 28 4 AFF4, BRWD1, BTG3, CELSR2, DNAJB6, LRIG1, MAP3K5, MAP4, MASTL, MCM7, MECP2, MIB1, NPAS2, OBFC2A, PARD6B, PFN2, PTHLH, RAPGEF4, RASD1, SCAMP2, SFRS2, SMOC2, TMEM64, VGLL3, WHSC1, YES1, ZFPM2, ZFYVE9 0.0074 hypermethylated
mir-519e 104 11 2 ARHGEF12, ARL4C, BCOR, CCNG2, CTDSPL2, DLL1, DPYSL5, EFNB3, NEDD4L, NPAS2, RAB35 0.0075 hypermethylated
mir-203 239 20 3 AFF4, BCL7A, CNTFR, CTDSPL2, DNMT3B, EGR1, FALZ, INSIG1, KCTD9, LASP1, MECP2, PLD2, PPM1B, RAPGEF4, SLC12A2, SMAD1, SPEN, SPIRE1, TCF12, YWHAQ 0.0064 hypomethylated
  1. MicroRNAs are listed that have statistically significant MeDIP differences between abuse and non-abuse groups whose predicted gene targets are enriched for gene promoters that are also differentially methylated between abuse and non-abuse groups. In each case, enrichment is for targets with lower methylation in the abused group.
  2. “enrichment p-value” indicates the level of enrichment for hypomethylated targets.
  3. “microRNA methylation” indicates whether the data predicts significantly higher (“hypermethylated”) or lower (“hypomethylated”) methylation levels in the abuse group.