Table 3.
Gene coexpression modules showing treatment specific associations at the genetic level.
| GCM characteristicsa | GCM-7* | GCM-10 |
|---|---|---|
| Module genes | 18 | 87 |
| Anti-TNF agent | Adalimumab | Infliximab |
| RespondersDisc (N) | 41 | 30 |
| Non-RespondersDisc (N) | 20 | 41 |
| RespondersRepl (N) | 438 | 289 |
| Non-RespondersRepl (N) | 171 | 244 |
| PDisc | 0.015 | 0.021 |
| SNPsDisc (N) | 5,321 | 1,473 |
| SNPsDiscSig (N) | 346 | 209 |
| SNPsDiscSigLD (N) | 18 | 18 |
| SNPsDisc | rs72681642, rs3104464, rs12135530, rs10782647, rs4562674, rs11165922, chr5:67561207, chr8:12854804, rs2454329, rs62187579, rs140900228, rs11165917, rs1519149, rs10061960, rs1550805, rs9677007, rs4949803, rs74105112 | rs934450, rs515247, rs1553544, rs2038442, rs11709521, rs7735205, rs55747890, rs4693803, rs6885000, rs632639, rs62234580, rs2341467, rs8074195, rs11097130, rs6777047, rs1148944, rs11117909, rs3803328, chr7:12288371, chr13:96078081 |
| PRepl | 0.0019 | 0.567 |
| SNPsRepl (N) | 15,270 | 3,760 |
| SNPsReplSig (N) | 573 | 135 |
| SNPsReplSigLD (N) | 20 | 20 |
| SNPsRepl | rs2297595, rs6593637, rs12047928, rs1709409, rs17100570, rs6685859, rs10747488, rs7414210, rs12037848, rs2466270, rs11102704, rs7169644, rs11165830, rs17379082, rs17784113, rs6863799, rs12567557, rs1992771 | rs16924328, rs6473297, rs4880181, rs7630022, rs3795039, rs1114518, rs2075814, rs2065394, rs259256, rs888246, rs10918341, rs867616, rs10407836, rs17024986, rs6766989, rs2380208, rs13159715, rs2072512, rs7853333, rs11977828 |
| PComb | 3.02e-4 | – |
Anti-TNF, anti-tumor necrosis factor treatment associated with the indicated gene coexpression module; Comb, combined p-value (i.e., p-value was only combined for the replicated associations); Disc, discovery cohort; GCM, gene coexpression module; P, empirical P-value obtained in the set-based genetic association analysis; N, sample size; Repl, replication cohort; Sig, nominally associated SNPs; LD, SNPs that are not in linkage disequilibrium (r2 < 0.02); SNP, single nucleotide polymorphism.
Characteristics of the gene coexpression modules that were found to be associated with the indicated treatment in the discovery cohort.
Replicated associations (P < 0.05 in both the discovery and replication cohorts).