Table 2. Hypo-methylated and up-regulated concordant epigenes.
| GeneID | Description | Symbol | Δ5 mc (%) | DS | FC | SM | ALSoD& OS |
| 58475 | membrane-spanning 4-domains, subfamily A, member 7 | MS4A7 | 6 | −19.0 | 4.6 | ||
| 1439 | colony stimulating factor 2 receptor, beta, low-affinity | CSF2RB | 6.6 | −35.4 | 3.8 | ||
| 9056 | solute carrier family 7 (amino acid transporter light chain, y+L system), member 7 | SLC7A7 | 6.6 | −18.6 | 3.5 | ||
| 822 | capping protein (actin filament), gelsolin-like | CAPG | 5.8 | −13.9 | 3.4 | ||
| 6556 | solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 | SLC11A1 | 8.6 | −34.4 | 3.1 | ||
| 54209 | triggering receptor expressed on myeloid cells 2 | TREM2 | 7.1 | −26.0 | 2.9 | ||
| 912 | CD1d molecule | CD1D | 5.6 | −19.7 | 2.8 | ✓ | |
| 10457 | glycoprotein (transmembrane) nmb | GPNMB | 10.1 | −43.1 | 2.8 | ✓ | |
| 2203 | fructose-1,6-bisphosphatase 1 | FBP1 | 7.7 | −96.5 | 2.7 | ||
| 11006 | leukocyte immunoglobulin-like receptor, subfamily B, member 4 | LILRB4 | 4.6 | −14.0 | 2.7 | ||
| 27036 | sialic acid binding Ig-like lectin 7 | SIGLEC7 | 5.3 | −15.9 | 2.7 | ✓ | |
| 4046 | lymphocyte-specific protein 1 | LSP1 | 6.4 | −20.1 | 2.7 | ||
| 864 | runt-related transcription factor 3 | RUNX3 | 7.5 | −32.8 | 2.6 | ||
| 11025 | leukocyte immunoglobulin-like receptor, subfamily B, member 3 | LILRB3 | 5.9 | −14.0 | 2.5 | ||
| 2207 | Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide | FCER1G | 5.5 | −20.2 | 2.4 | ||
| 10261 | immunoglobulin superfamily, member 6 | IGSF6 | 10.2 | −50.2 | 2.3 | ||
| 286256 | lipocalin 12 | LCN12 | 5.2 | −18.4 | 2.3 | ||
| 1230 | chemokine (C-C motif) receptor 1 | CCR1 | 7.3 | −25.2 | 2.3 | ||
| 51225 | ABI family, member 3 | ABI3 | 6.3 | -19.2 | 2.3 | ||
| 1522 | cathepsin Z | CTSZ | 5.8 | −39.3 | 2.2 | ✓ | |
| 26157 | GTPase, IMAP family member 2 | GIMAP2 | 7.2 | −35.0 | 2.2 | ||
| 10023 | frequently rearranged in advanced T-cell lymphomas | FRAT1 | 5.2 | −46.0 | 2.2 | ||
| 1117 | chitinase 3-like 2 | CHI3L2 | 7.1 | −22.6 | 2.1 | ||
| 64344 | hypoxia inducible factor 3, alpha subunit | HIF3A | 5.8 | −48.9 | 2.1 | ||
| 10320 | IKAROS family zinc finger 1 (Ikaros) | IKZF1 | 6.8 | −22.2 | 2.1 | ||
| 1051 | CCAAT/enhancer binding protein (C/EBP), beta | C/EBPB | 4.9 | −54.7 | 2.1 | ||
| 1601 | disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila) | DAB2 | 3.9 | −13.7 | 2.0 | ||
| 84898 | plexin domain containing 2 | PLXDC2 | 3 | −23.7 | 2.0 | ||
| 10990 | leukocyte immunoglobulin-like receptor, subfamily B, member 5 | LILRB5 | 7.5 | −36.6 | 2.0 | ||
| 254295 | phytanoyl-CoA dioxygenase domain containing 1 | PHYHD1 | 3.1 | −13.6 | 1.9 | ||
| 4488 | msh homeobox 2 | MSX2 | 5.4 | −51.9 | 1.9 | ||
| 558 | AXL receptor tyrosine kinase | AXL | 3.3 | −14.5 | 1.8 | ||
| 5359 | phospholipid scramblase 1 | PLSCR1 | 7.3 | −82.6 | 1.8 | ||
| 23526 | histocompatibility (minor) HA-1 | HMHA1 | 0 | −33.5 | 1.8 | ||
| 50856 | C-type lectin domain family 4, member A | CLEC4A | 9.5 | −45.3 | 1.7 | ||
| 116843 | chromosome 6 open reading frame 192 | C6orf192 | 3.4 | −16.5 | 1.7 | ||
| 55544 | RNA binding motif protein 38 | RBM38 | 4.9 | −20.8 | 1.7 | ||
| 23209 | megalencephalic leukoencephalopathy with subcortical cysts 1 | MLC1 | 7.4 | −29.0 | 1.7 | ||
| 23418 | crumbs homolog 1 (Drosophila) | CRB1 | 6.2 | −15.2 | 1.7 | ||
| 1501 | catenin (cadherin-associated protein), delta 2 | CTNND2 | 2.9 | −18.0 | 1.6 | ||
| 5045 | furin (paired basic amino acid cleaving enzyme) | FURIN | 5.9 | −19.7 | 1.6 | ✓ | ✓ |
| 1317 | solute carrier family 31 (copper transporters), member 1 | SLC31A1 | 5.3 | −19.4 | 1.6 | ✓ | |
| 123920 | CKLF-like MARVEL transmembrane domain containing 3 | CMTM3 | 3.9 | −16.6 | 1.6 | ||
| 6776 | signal transducer and activator of transcription 5A | STAT5A | 4.2 | −16.6 | 1.6 | ||
| 57522 | SLIT-ROBO Rho GTPase activating protein 1 | SRGAP1 | 0.3 | −43.9 | 1.5 | ||
| 9404 | leupaxin | LPXN | 4 | −13.9 | 1.5 | ||
| 122618 | phospholipase D family, member 4 | PLD4 | 5.5 | −18.0 | 1.5 | ||
| 64859 | oligonucleotide/oligosaccharide-binding fold containing 2A | OBFC2A | 7.2 | −99.8 | 1.5 | ||
| 10628 | thioredoxin interacting protein | TXNIP | 4.3 | −26.1 | 1.4 | ||
| 79939 | solute carrier family 35, member E1 | SLC35E1 | 0 | −46.6 | 1.3 | ||
| 5660 | prosaposin | PSAP | 0 | −33.5 | 1.3 |
Genes are ordered by expression fold change (FC). Percent methylation change (Δ5 mc (%)) is calculated by |BetaALS – Betacontrol|/Betacontrol. DiffScore (DF), Differential methylation (a transformation of the p-value; p = 0.05, p = 0.01, p = 0.001 are equivalent to DiffScore = ±13, ±20, ±30, respectively). Fold change (FC) in gene expression ‘✓’ indicates that the corresponding gene was identified as an ALS-associated gene by SciMiner (SM), the ALSoD database, and other high-throughput microarray studies (OS) on human ALS spinal cord samples, respectively. See Table S2 more details.