TABLE 2.
MSigDB immunologic signatures associated with differences between blood cell types
| Ontology | Enriched terms of differentially methylated fragments (2014) | Binomial FDR q | Observed gene hits (n) | Total genes (n) |
|---|---|---|---|---|
| Low methylation in ALS | ||||
| MSigDB perturbation | Genes up-regulated in NBA cells (APL) in response to tretinoin (PubChem 444795); based on ChIP-seq data | 3.39E-08 | 124 | 781 |
| MSigDB perturbation | Genes up-regulated in the human mammary epithelial cells upon expression of TP53 (GeneID 7157) off adenoviral vector | 3.30E-08 | 156 | 1065 |
| MSigDB immunologic signatures | Genes down-regulated in comparison of monocytes treated with 1 ng/ml LPS (TLR4 agonist) vs. monocytes treated with vehicle. | 2.25E-03 | 38 | 192 |
| MSigDB immunologic signatures | Genes down-regulated in comparison of healthy CD4 (GeneID 920) T cells vs. healthy myeloid cells | 1.44E-03 | 38 | 197 |
| MSigDB immunologic signatures | Genes down-regulated in comparison of monocytes treated with anti-TREM1 (GeneID 54210) vs. monocytes treated with vehicle | 1.28E-03 | 38 | 193 |
| MSigDB immunologic signatures | Genes down-regulated in comparison to healthy B cells vs. healthy myeloid cells | 1.88E-02 | 35 | 198 |
| MSigDB immunologic signatures | Genes up-regulated in comparison of dendritic cells vs. central memory CD4 (GeneID 920) T cells | 2.64E-02 | 34 | 197 |
| High methylation in ALS | ||||
| MSigDB perturbation | Genes up-regulated in NB4 cells (APL) in response to tretinoin (PubChem 444795); based on ChIP-seq data | 1.59E-08 | 111 | 781 |
| MSigDB perturbation | Genes with high-CpG-density promoters (HCPs) bearing the trimethylation marker at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state) | 2.58E-08 | 71 | 418 |
| MSigDB perturbation | Genes within amplicon 16p13 identified in a study of 191 breast tumor samples. | 5.91E-03 | 22 | 110 |
| MSigDB perturbation | Genes up-regulated in comparison of naive CD4 (GeneID 920) T cells vs. d 0 monocytes | 4.01E-02 | 30 | 187 |
Top and bottom 1000 differentially methylated fragments ranked by the difference in fragment mediation between the ALS twin and the unaffected twin 2014 samples were subjected to GREAT for 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.