TABLE 1.
DNA Methylation differences between the twins related to the H3K27me3 marker
| Ontology | Enriched terms of differentially methylated fragments (2013) | Binomial FDR q | Observed gene hits (n) | Total genes (n) |
|---|---|---|---|---|
| Low methylation in ALS | ||||
| MSigDB perturbation | Genes up-regulated in NB4 cells (APL) in response to tretinoin (PubChem 444795); based on ChIP-seq data | 5.11E-30 | 111 | 781 |
| MSigDB perturbation | Genes with high-CpG-density promotors (HCPs) bearing a histone H3 trimethylation marker at K27 (H3K27me3) in MEF cells (embryonic fibroblast) | 5.30E-23 | 87 | 573 |
| High methylation in ALS | ||||
| MSigDB perturbation | Genes up-regulated in NB4 cells (APL) in response to tretinoin (PubChem 444795); based on ChIP-seq data | 2.61E-33 | 101 | 781 |
| MSigDB perturbation | Genes with HCPs bearing the trimethylation marker, at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state) | 1.51E-27 | 70 | 418 |
Top and bottom 1000 differentially methylated fragments ranked by the difference in fragment methylation between the ALS twin and the unaffected twin 2013 samples were subjected to GREAT enrichment testing in the MSigDB perturbation and MSigDB immunologic signatures. The 5 most enriched terms for each ontology are reported, with a minimum FDR < 0.05.