Table 3.
Methylation of microRNAs and their target genes
| 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 |
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.
“enrichment p-value” indicates the level of enrichment for hypomethylated targets.
“microRNA methylation” indicates whether the data predicts significantly higher (“hypermethylated”) or lower (“hypomethylated”) methylation levels in the abuse group.