TABLE 3.
Four high-level functions associated with genes differentially methylated between monozygotic twins and unaffected siblings and identified by CpG island microarray
| Category and no. genes | Function annotation | Molecules | P value |
|---|---|---|---|
| Gene expression; 30 | Transcription | ATF1, CBX2, CCNB1, CHAF1A, FOXN3, FRAT1, ILK, IRF1, ITGA5, MED7 (includes EG:9443), MEIS1, MLLT1, MTPN, MYF6, NFIA, NR2C1, PAX7, PWP1, RBM39, RORA, RREB1, RRN3, SET, TFDP2, TG, TGFBR2, VDR, ZNF234 | 9.02E-08 |
| Transactivation | ATF1, FRAT1, IRF1, NFIA, PAX7, RBM39, RORA, TFDP2, TGFBR2, VDR | 1.92E-03 | |
| Activation of TGF beta response element | ITGA5, TGFBR2 | 4.93E-03 | |
| Transactivation of response element | VDR | 5.29E-03 | |
| Transactivation of RORE binding site | RORA | 5.29E-03 | |
| Expression of DNA endogenous promoter | TG, VDR | 7.06E-03 | |
| Activation of Atf-1 binding site | ATF1 | 1.05E-02 | |
| Activation of NFI binding site | NFIA | 1.05E-02 | |
| Binding of TREpal motif | VDR | 1.05E-02 | |
| Transcription of beta catenin response element | FRAT1 | 1.05E-02 | |
| Activation of HAF1/HAF1a binding site | IRF1 | 1.58E-02 | |
| Activation of IRF1/IRF2 binding site | IRF1 | 1.58E-02 | |
| Binding of NFAT response element | VDR | 1.58E-02 | |
| Cell death; 24 | Apoptosis | ATF1, BAK1, CCNB1, CDC73, FAS, FRAT1, FXR1, GRIA2, GULP1, HPN, ILK, IRF1, ITGA5, MCF2L, MED7, MTPN, PAX7, PLA2G6, RRN3, TGFBR2, TIAM1, VDR | 4.30E-03 |
| Delay in cell death of cortical neurons | BAK1 | 5.29E-03 | |
| Killing of oligodendrocytes | MBP | 5.29E-03 | |
| Cell death of microglia | FAS, IRF1 | 5.43E-03 | |
| Apoptosis of embryonic cells | ATF1, FAS, ITGA5 | 6.02E-03 | |
| Cell death | ATF1, BAK1, CCNB1, CDC73, FAS, FRAT1, FXR1, GRIA2, GULP1, HPN, ILK, IRF1, ITGA5, MBP, MCF2L, MED7, MEIS1, MTPN, PAX7, PLA2G6, RRN3, TGFBR2, TIAM1, VDR | 6.61E-03 | |
| Apoptosis of embryonic stem cells | FAS, ITGA5 | 7.65E-03 | |
| Cell death of brain cells | BAK1, FAS, FRAT1, GRIA2 | 2.54E-02 | |
| Cell death of cortical neurons | BAK1, FAS, GRIA2 | 2.56E-02 | |
| Neurological disease (12) | Delay in cell death of cortical neurons | BAK1 | 5.29E-03 |
| Killing of oligodendrocytes | MBP | 5.29E-03 | |
| Neurodegeneration of CA3 neurons | GRIA2 | 5.29E-03 | |
| Cell death of microglia | FAS, IRF1 | 5.43E-03 | |
| Disease of brain cells | GRIA2, TG | 1.02E-02 | |
| Depletion of neurons | DLD | 1.05E-02 | |
| Gracile axonal dystrophy | PLA2G6 | 1.05E-02 | |
| Mobility of brain cancer cell lines | ITGA5 | 1.05E-02 | |
| Multiple sclerosis of humans | MBP | 1.58E-02 | |
| Deurodegeneration | GRIA2, PLA2G6, TGFBR2 | 1.76E-02 | |
| Apoptosis of granule cells | FAS, FRAT1 | 1.89E-02 | |
| Cell death of brain cells, cortical neurons | BAK1, FAS, FRAT1, GRIA2 | 2.54E-02 | |
| Apoptosis of neural precursor cells | FAS | 2.62E-02 | |
| Hypomyelination of axons | MBP | 2.62E-02 | |
| Nervous system development and function; 6 | Calcium permeability of neurons, innervation of Purkinje cells, retraction of glial cell projections | GRIA2 | 5.29E-03 |
| Formation of hippocampal commissure, presence/development of corpus callosum, formation of sling cells | NFIA | 5.29E-03 | |
| Dedepression and depotentiation of CA1 neurons | GRIA2 | 1.05E-02 | |
| Organization of axons, organization of central nervous system | MBP | 1.05E-02 | |
| Quantity of satellite cells | PAX7 | 1.05E-02 | |
| Cilation of cerebral ventricles | NFIA | 1.58E-02 | |
| Function of brain | RORA | 2.10E-02 | |
| Formation of neurite branches | TIAM1 | 2.10E-02 | |
| Migration of neuroglia | NFIA, TIAM1 | 2.26E-02 |
P values represent significance by Fisher’s exact test and indicate the probability that the indicated function is not associated with the dataset of differentially methylated genes (Ingenuity Pathway Analysis software).