TABLE V.
DMRs for asthma in relation to childhood methylation with adjustment for covariates and cell type identified by using both comb-p (P < .01) and DMRcate (FDR < 0.01) methods
| chromosome:position | Gene name* | No. of CpGs in region | P value from comb-p† | FDR from DMRcate‡ |
|---|---|---|---|---|
| Chr 1: 161575716-161576323 | HSPA7 | 4 | 8.61E-03 | 1.24E-03 |
| Chr 1: 209979111-209979780 | IRF6 | 13 | 4.62E-04 | 1.90E-04 |
| Chr 1: 2036283-2036644 | PRKCZ | 4 | 2.00E-04 | 3.14E-05 |
| Chr 1: 87596820-87596935 | LINC01140 | 3 | 1.58E-03 | 2.79E-05 |
| Chr 2: 149639612-149640260 | KIF5C | 4 | 3.50E-03 | 1.14E-05 |
| Chr 2: 11917490-11917788 | LPIN1 | 3 | 4.81E-03 | 6.25E-04 |
| Chr 3: 195974258-195974330 | PCYT1A | 3 | 5.07E-05 | 2.00E-05 |
| Chr 3: 3151795-3152917 | IL5RA | 6 | 1.35E-08 | 2.12E-09 |
| Chr 5: 38445220-38446193 | EGFLAM | 9 | 5.11E-06 | 1.28E-05 |
| Chr 5: 132008525-132009631 | IL4 | 4 | 5.36E-07 | 3.11E-05 |
| Chr 6: 112688010-112688931 | RFPL4B | 4 | 4.89E-05 | 5.19E-04 |
| Chr 6: 166876490-166877039 | RPS6KA2;RPS6KA2-IT1 | 8 | 3.08E-05 | 1.74E-06 |
| Chr 7: 156735383-156735657 | NOM1 | 3 | 7.11E-03 | 2.82E-03 |
| Chr 7: 149543136-149543178 | ZNF862 | 3 | 3.85E-16 | 1.43E-16 |
| Chr 7: 65419185-65419289 | VKORC1L1 | 7 | 2.82E-03 | 1.04E-03 |
| Chr 8: 832917-833049 | ERICH1-AS1;DLGAP2 | 3 | 6.15E-03 | 6.44E-03 |
| Chr 8: 141046436-141046853 | TRAPPC9 | 5 | 8.93E-07 | 3.45E-09 |
| Chr 9: 138362321-138362505 | PPP1R26-AS1 | 3 | 2.72E-05 | 1.44E-09 |
| Chr 9: 130859454-130859607 | SLC25A25 | 2 | 2.69E-08 | 5.84E-08 |
| Chr 11: 65545808-65547173 | AP5B1 | 8 | 1.31E-10 | 9.73E-12 |
| Chr 11: 69291998-69292065 | LINC01488 | 3 | 4.55E-04 | 1.65E-04 |
| Chr 11: 59856225-59856359 | MS4A2 | 2 | 1.50E-03 | 3.25E-04 |
| Chr 12: 15125458-15126021 | PDE6H | 4 | 6.93E-03 | 7.65E-06 |
| Chr 14: 100610071-100610668 | EVL | 6 | 7.79E-16 | 1.24E-19 |
| Chr 15: 64275810-64275854 | DAPK2 | 2 | 4.91E-04 | 2.04E-04 |
| Chr 15: 99443213-99443667 | IGF1R | 4 | 6.57E-05 | 2.41E-04 |
| Chr 16: 875257-875627 | PRR25 | 4 | 3.34E-03 | 3.21E-03 |
| Chr 16: 88539861-88540397 | ZFPM1 | 5 | 1.09E-04 | 1.13E-05 |
| Chr 16: 615709-616221 | PRR35 | 5 | 1.62E-04 | 2.70E-07 |
| Chr 16: 85551478-85551749 | GSE1 | 3 | 5.27E-07 | 2.37E-07 |
| Chr 17: 56269410-56270829 | EPX | 5 | 6.20E-11 | 1.41E-08 |
| Chr 17: 78682785-78683458 | RPTOR | 5 | 1.18E-04 | 4.03E-04 |
| Chr 19: 51961666-51961938 | SIGLEC8 | 3 | 2.37E-04 | 5.07E-04 |
| Chr 19: 50553682-50554511 | LOC400710 | 10 | 1.78E-07 | 3.81E-06 |
| Chr 20: 35503832-35504554 | TLDC2 | 8 | 1.23E-03 | 5.90E-08 |
| Chr 21: 42520365-42520903 | LINC00323 | 3 | 1.41E-04 | 2.64E-05 |
*
DMRcate annotates to UCSC RefGene from Illumina annotation file. The first listed gene is shown.
†
Comb-p uses a 1-step Sidak multiple-testing correction on the regional P value assigned by using the Stouffer-Liptak method.
‡
DMRcate takes the minimum Benjamini-Hochberg FDR-corrected P value in the region as representative after recalculating P values by using Gaussian kernel smoothing.