Table 3.
Overlapping findings between the existing literature and the work presented in this studya.
| Literature |
This study |
|||
|---|---|---|---|---|
| Gene(s), reference | Description | Gene/domain | Description/interaction | Network/pathwayb |
| a. Genetics | ||||
| CYP11A, CYP17 (37–39) | Cytochrome P450 family members 11A and 17 | CYP2C8, CYP2F1 | Cytochrome P450 family members 2C8, 2F1 | Network: 1, 6 |
| Pathway: FXR/RXR Activation | ||||
| TNF (37–39) | Tumor necrosis factor | TNFRSF1A, TNFRSF1B | Tumor necrosis factor receptor superfamily members 1A and 1B | Network: 5 |
| Pathway: Type I and Type II Diabetes Mellitus | ||||
| PPARG (37–39) | Peroxisome proliferator-activated receptor gamma | PPAR/RXRA | Heterodimer regulating transcription | Network: 1, 3, 5, 6, 9, 10 |
| Pathway: PPAR/RXRA Activation | ||||
| RAB5B (40) | RAS oncogene family member 5B | RAB19 | RAS oncogene family member 19 | Network: 9 |
| Pathway: – | ||||
| ZNF557 (40) | Zinc finger protein member 557 | ZNF71, ZNF331, ZNF446, ZNF586 | Zinc finger protein members 71, 331, 446, 586 | Network: 1, 3, 4, 6, 7, 8 |
| Pathway: – | ||||
| STXBP1 (41) | Syntaxin binding protein 1 | STXBP2 | Syntaxin binding protein 2 | Network: 1 |
| Pathway: – | ||||
| LAMA1 (44, 45) | Laminin chain alpha 1 | LAMA5, LAMB2 | Laminin chain alpha 5, beta 2 | Network: 9 |
| Pathway: CDK5 signaling | ||||
| b. Epigenetics | ||||
| CYP19A1 (42, 43) | Cytochrome P450 family member 19A1 | CYP2C8, CYP2F1 | Cytochrome P450 family members 2C8, 2F1 | Network: 1, 6 |
| Pathway: FXR/RXR Activation | ||||
| HOXA10 (42, 43) | Homeobox member A10 | HOXA7 | Homeobox member A7 | Network: 3 |
| Pathway: – | ||||
| IGF2BP2 (42, 43) | Insulin-like growth factor 2 mRNA binding protein 2 | IGF2BP2 | Insulin-like growth factor 2 mRNA binding protein 2 | Network: 3 |
| Pathway: – | ||||
| LHCGR (42, 43) | Luteinizing hormone/choriogonadotropin receptor | LHCGR | Luteinizing hormone/choriogonadotropin receptor | Network: 2 |
| Pathway: G-Protein Coupled Receptor Signaling | ||||
| PDE4D (42, 43) | Phosphodiesterase family member 4D | PDE4A, PDE4D, PDE11A | Phosphodiesterase family members 4A, 4D, 11A | Network: 4 |
| Pathway: G-Protein Coupled Receptor Signaling | ||||
| SLC7A8 (42, 43) | Solute carrier family member 8 | SLC2A9, SLC6A1, SLC6A4, SLC7A4, SLC7A8, SLC12A5, SLC14A1, SLC16A3, SLC22A18, SLC25A23, SLC27A1, SLC29A1, SLC43A2 | Solute Carrier Family members 2A9, 6A1, 6A4, 7A4, 7A8, 12A5, 14A1, 16A3, 22A18, 25A23, 27A1, 29A1, 43A2 | Network: 1, 2, 3, 5, 6, 7, 8, 10 |
| Pathway: – | ||||
aFor those comparisons where literature findings refer to genes that are part of large gene families for which we identified differential methylation on some gene members, we carried out a confirmatory Ingenuity Pathway Analysis (IPA) (data not shown). We analyzed all genes of the same family reported in the table by running independent IPA analyses by gene family. By using the more stringent setup that generates 35-items networks, which is ideal for small gene lists as networks get generated only if genes have direct and more relevant connections, each gene family from our list only generated one 35-item network. This test supports our approach that is meant at showing that alterations of the methylation status of the genes presented here, and belonging to the same gene families, affect gene networks that have been shown to work together to carry out specific cellular functions.
bPathways are reported when univocal or when known.