Table 2. In silico evidence for edges from functional network of IgG N-glycosylation loci.
Permutation analysis was used to assess the distribution of glycome-wide SNP effect pairwise correlations and the STRING PPI database (16) to search for biological validation of observed links. All reported correlations are statistically significant after Bonferroni correction. Corr, Spearman’s correlation coefficient of z scores of SNP1 and z scores of SNP2; quant, quantile of distribution at which the given ρ2 was observed in permutation analysis; STRING score, probability that the link exists obtained by combining evidence from different sources. SNPs that were replicated in UPLC replication are in bold.
| SNP1 | SNP2 | Locus 1 | Locus 2 | Corr | SNP 1 quant | SNP 2 quant |
STRING gene 1 |
STRING gene 2 |
STRING score |
| Glycosyltransferase loci | |||||||||
| rs5750830 | rs17630758 | MGAT3 | SMARCB1-DERL3-CHCHD10-VPREB3 | 0.967 | 0 | 0 | |||
| rs10813951 | rs12341905 | B4GALT1 | SPINK4 | 0.805 | 3.54 × 10−3 | 7.72 × 10−3 | |||
| rs10813951 | rs7758383 | B4GALT1 | HIVEP2 | 0.711 | 1.87 × 10−2 | 3.83 × 10−3 | |||
| rs7621161 | rs481080 | ST6GAL1 | NXPE1; NXPE4 | 0.773 | 6.00 × 10−5 | 3.01 × 10−3 | |||
| rs7621161 | rs7700895 | ST6GAL1 | ELL2 | 0.581 | 8.32 × 10−3 | 2.45 × 10−2 | |||
| rs11847263 | rs7216389 | FUT8 | ORMDL3-GSDMB-IKZF3-ZPBP2 | 0.709 | 8.42 × 10−3 | 2.59 × 10−2 | |||
| rs11847263 | rs6421315 | FUT8 | IKZF1 | 0.624 | 2.62 × 10−2 | 9.69 × 10−2 | |||
| Other loci | |||||||||
| rs10903118 | rs7281587 | RUNX3 | RUNX1 | 0.891 | 2.00 × 10−5 | 3.00 × 10−5 | RUNX3 | RUNX1 | 0.9 |
| rs7281587 | rs17630758 | RUNX1 | SMARCB1-DERL3-CHCHD10-VPREB3 | 0.597 | 3.25 × 10−2 | 1.59 × 10−2 | RUNX1 | SMARCB1 | 0.4 |
| rs10903118 | rs17630758 | RUNX3 | SMARCB1-DERL3-CHCHD10-VPREB3 | 0.694 | 1.15 × 10−2 | 3.33 × 10−3 | |||
| rs7216389 | rs6421315 | ORMDL3-GSDMB-IKZF3-ZPBP2 | IKZF1 | 0.609 | 9.57 × 10−3 | 2.49 × 10−2 | IKZF3 | IKZF1 | 0.42 |
| rs7216389 | rs6421315 | ORMDL3-GSDMB-IKZF3-ZPBP2 | IKZF1 | 0.609 | 9.57 × 10−3 | 2.49 × 10−2 | ZPBP2 | IKZF1 | 0.48 |
| rs7281587 | rs6421315 | RUNX1 | IKZF1 | 0.626 | 2.56 × 10−2 | 2.15 × 10−2 | IKZF1 | RUNX1 | 0.6 |
| rs11748193 | rs3099844 | IRF1-SLC22A4 | TCF19-GPANK1-TNXB-HLA-DRA | 0.231 | 8.82 × 10−2 | 9.86 × 10−2 | HLA-DRA | IRF1 | 0.93 |
| rs7281587 | rs11748193 | RUNX1 | IRF1-SLC22A4 | 0.283 | 1.63 × 10−1 | 6.02 × 10−2 | RUNX1 | SLC22A4 | 0.7 |
| rs7257072 | rs3099844 | RFXANK | TCF19-GPANK1-TNXB-HLA-DRA | 0.23 | 1.77 × 10−1 | 9.85 × 10−2 | HLA-DRA | RFXANK | 0.62 |