Table 3. Top gene sets enriched for hypermethylated genes in SS.
| gene set | n | overlap genes | p-value | adj. p-value |
|---|---|---|---|---|
| Positive regulation of transporter activity | 6 | WNK4, ATP1B2, RELN, HAP1, CACNB2, TRPC6 | 1.36E-8 | 6.12E-5 |
| Diencephalon development | 5 | ETS1, GSX1, GLI2, HAP1, SLC6A4 | 4.17E-7 | 9.38E-4 |
| Hypothalamus development | 3 | ETS1, GSX1, HAP1 | 1.73E-6 | 2.59E-3 |
| Vasoconstriction | 3 | EDN3, HTR1A, SLC6A4 | 3.29E-6 | 3.42E-3 |
| Modulation of excitatory postsynaptic potential | 3 | ZMYND8, CELF4, RELN | 4.38E-6 | 3.42E-3 |
| Somatic stem cell population maintenance | 4 | WNT98, LRP5, PBX1, BCL9 | 4.59E-6 | 3.42E-3 |
| Nerve development | 4 | HOXB3, COL25A1, TFAP2A, SLITRK6 | 5.32E-6 | 3.42E-3 |
| Peptide Transport | 4 | EDN3, SLC15A2, FAM3B, TAPBP | 7.06E-6 | 3.97E-3 |
| Anatomical structure regression | 2 | LRP5, GLI2 | 1.03E-5 | 4.86E-3 |
| ERBB2 signaling pathway | 3 | ERBB2, GRB7, SHC1 | 1.28E-5 | 4.86E-3 |
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.