Table 2.
Differentially methylated positions associated with type 2 diabetes (T2D) with and without adjustment for body mass index (BMI)
| Base model |
Adjusted for BMI |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| CpG | CHR | Position | Genea | Featureb | Delta β-valuec | P-valued | FDRd | BACON FDRe | P-valued | FDRd | BACON FDRe |
| cg19693031 | 1 | 145 441 552 | TXNIP | 3’UTR | −0.0408 | 7.35E-18 | 3.15E-12 | 3.62E-12 | 2.45E-17 | 1.05E-11 | 8.28E-10 |
| cg04816311 | 7 | 1 066 650 | C7orf50 | Body | 0.0198 | 1.96E-09 | 4.21E-04 | 2.03E-03 | 1.99E-09 | 4.28E-04 | 1.22E-02 |
| cg00574958 | 11 | 68 607 622 | CPT1A | 5’UTR | −0.0159 | 9.26E-08 | 1.32E-02 | 1.84E-02 | 3.09E-06 | 1.66E-01 | 8.00E-01 |
| cg07988171 | 19 | 16 199 419 | TPM4 | Body | −0.0176 | 3.44E-07 | 3.69E-02 | 4.98E-02 | 2.73E-06 | 3.68E-02 | 2.47E-01 |
| cg07477137 | 11 | 65 083 332 | CDC42EP2 | 5’UTR | 0.0044 | 6.36E-07 | 4.64E-02 | 1.66E-01 | 5.86E-07 | 6.29E-02 | 7.62E-01 |
| cg03078690 | 6 | 33 235 504 | VPS52 | Body | 0.0089 | 6.48E-07 | 4.64E-02 | 1.66E-01 | 6.05E-06 | 1.96E-01 | 9.56E-01 |
a
CpGs are located in the gene if no distance is indicated (genome build Hg19).
b
Based on manifest feature annotation Illumina.
c
Beta coefficients were computed from methylation beta-values. Negative beta-values indicate lower DNA methylation (hypomethylation) in cases compared with controls.
d
P-values and FDRs corresponding to M-values.
e
FDRs corresponding to M-values for the models corrected for inflation by possible systematic biases using the BACON method. Results are sorted on P-values for the BACON-adjusted base model.
CHR, Chromosome.