Table 2. Top gene sets enriched for hypomethylated genes in SS.
| gene set | n | overlap genes | p-value | adj. p-value |
|---|---|---|---|---|
| SS DMP genes | 8 | TAP1, LTA, PSMB8, AIM2, NCKAP1L, LINC00426, LCP2, ARHGAP25 | 3.80E-18 | 1.71E-14 |
| Antigen processing and presentation of endogenous peptide antigen | 4 | HLA-E, HLA-B, TAP1, ABCB1 | 1.60E-12 | 3.59E-9 |
| Antigen processing and presentation of peptide antigen via MHC class I | 6 | PSMB9, HLA-E, PSMB8, HLA-B, TAP1, ABCB1 | 4.74E-12 | 5.53E-9 |
| Antigen processing and presentation of endogenous antigen | 4 | HLA-E, HLA-B, TAP1, ABCB1 | 4.92E-12 | 5.53E-9 |
| Negative regulation of innate immune response | 4 | HLA-E, HLA-B, TAP1, NLRC5 | 3.93E-10 | 3.24E-7 |
| Negative regulation of natural killer cell mediated immunity | 3 | HLA-E, HLA-B, TAP1 | 4.32E-10 | 3.24E-7 |
| Antigen processing and presentation via MHC class IB | 3 | HLA-E, TAP1, ABCB1 | 1.19E-10 | 7.64E-7 |
| Positive regulation of antigen processing and presentation | 3 | ABCB1, CCR7, TAP1 | 1.58E-9 | 7.92E-7 |
| Positive regulation of humoral immune response | 3 | LTA, TNF, CCR7 | 1.58E-9 | 7.92E-7 |
| Negative regulation of cell killing | 3 | HLA-B, HLA-E, TAP1 | 2.66E-9 | 1.20E-6 |
Candidate gene sets include GO gene sets from the Molecular Signatures Database [44], a set of genes previously reported to harbor differentially methylated CpG sites between SS cases and non-cases (SS DMP genes) [20], and a set of genes previously reported to be differentially expressed between SS cases and healthy controls (SS DE genes) [54]. n = number of overlapping genes; adj. p-value = Benjamini-Hochberg adjusted p-value.