Table 3. High-hubs, hubs, VIPs and community in Early and/or Late CO networks.
| Early | Late | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene | Comm 1 | Cat 2 | K0 | K1 | Comm | Cat | K0 | K1 | Gene function/product [reference] |
| DPYD | B | Hub | 240 | 1361 | Dihydropyrimidine dehydrogenase involved in pyrimidine catabolism and modulation of beta-alanine production [146] | ||||
| STX6 | B | Hub | 213 | 1072 | t-SNARE family member that regulates intracellular membrane trafficking [149] | ||||
| DST | B | Hub | 185 | 994 | Cytoskeletal-associated protein essential for maintaining neuronal cytoskeleton organization [150] | ||||
| BDP1 | C | Hub | 216 | 1342 | Aliase: TFIIIB. Subunit of the TFIIIB transcription initiation complex; essential component of human TFIIIC activity [195,110] | ||||
| ZNF417 | C | VIP | 75 | 2171 | Zinc finger protein (Gene ID: 147687) | ||||
| ZNF429 | C | VIP | 41 | 1821 | DNA-binding protein associated with analgesic onset in humans [207] | ||||
| MCTS1 | C | VIP | 40 | 1788 | Aliase: MCT1.Carboxylate transporter; its deficiency was observed in human epileptogenic hippocampus [115] | ||||
| GRLF1 | C | High-hub | 408 | 2221 | Aliase: ARHGAP35. Rho-GTPase involved in the promotion of neurite outgrowth [119] | ||||
| ANKS1B | C | High-hub | 117 | 2494 | Aliase: AIDA1.Postsynaptic scaffolding protein linking signal events occurring at neuronal synapse with global changes in gene expression [118] | ||||
| PCF11 | C | High-hub | 115 | 2443 | 3’-end processing factor enhancing RNA polymerase II nascent RNA degradation and transcriptional termination [120] | ||||
| C6orf25 | D | Hub | 217 | 1182 | Aliase: G6bB. Inhibitory platelet receptor bearing ITAM and ITIM motifs; modulates microglia-neuron interaction[126, 127] | ||||
| PNPLA7 | D | Hub | 181 | 862 | Patatin-like 7hospholipase involved in lipid/energy homeostasis and axonal and synaptic integrity [129, 130,127] | ||||
| C20orf149 | D | VIP | 36 | 2384 | Aliase: PPDPF. Pancreatic progenitor cell differentiation and proliferation factor (gene ID 79144) | ||||
| RPL6 | D | VIP | 46 | 2092 | Ribosomal protein L6 regulates HDM2—p53 pathway in response to ribosomal stress [124] | ||||
| LOC142937 | D | VIP | 34 | 1837 | Uncharacterized gene products BC008131 (Gene ID: 142937) | ||||
| DTWD2 | D | VIP | 41 | 1837 | Prothymosin alpha involved in response to oxidative stress and neuronal survival [125] | ||||
| ZNF664 | D | High-hub | 135 | 2800 | Zinc finger protein 664 (Gene ID: 144348) | ||||
| ZNF546 | D | High-hub | 136 | 2144 | Zinc finger protein 546 (Gene ID: 339327) | ||||
| DNAJB2 | D | High-hub | 123 | 1747 | Aliase: HSP70. heat-shock protein expressed in hippocampal neurons; stress marker of TLE [121] | ||||
| MTR | D | High-hub | 130 | 1728 | Regulation of homocysteine, an excitatory amino acid, protecting hippocampal neurons against oxidative stress [122, 123] | ||||
| LOC402176 | E | Hub | 179 | 697 | Aliase: RPL21. Ribosomal protein L21 (Gene ID: 6144) | ||||
| ASPA | H | Hub | 220 | 1150 | Aspartoacylase, catabolizes NAA (N-acetyil-L-aspartic acid) in oligodendrocytes; responsive to glutamatergic activity [144] | ||||
| SMA4 | H | VIP | 79 | 2299 | Aliase: SMN1. SMN protein that modulates neuronal survival [132] | ||||
| RAD54L2 | H | VIP | 39 | 1793 | Aliase: ARIP4. Chromatin remodeling factor; modulates excitation/inhibition balance in hippocampal neurons towards seizure inhibition [133] | ||||
| ELF2 | H | VIP | 28 | 1737 | E1f transcription factor;promotes cell survival under cytokine stress [134] | ||||
| ATF4 | H | High-hub | 139 | 2142 | Transcription factor mediating neuronal resistance against oxidative stress [136, 137] | ||||
| LENG1 | H | High-hub | 125 | 2109 | Leukocyte receptor cluster (LRC) member 1 [140] | ||||
| YKT6 | H | High-hub | 123 | 1970 | Conserved SNARE essential for ER-Gogi transport, highly expressed in neurons and enriched in hippocampus [141] | ||||
| SERPINB2 | H | High-hub | 130 | 1840 | Synaptic activity-induced neuroprotection against seizure-induced brain-damage [143] | ||||
| RPL34 | J | Hub | 171 | 529 | Ribosomal protein L34, a Cdk5 inhibitor [151] | ||||
| RBMX | S | Hub | 152 | 764 | RNA binding motif protein involved in the promotion of neurite growth [154] | ||||
| MLXIP | B | Hub | 318 | 3089 | Aliase: MondoA. glucose sensing transcription factor involved in glucose homeostasis [178] | ||||
| ZIC5 | C | Hub | 291 | 3523 | C2H2-type zinc finger protein involved in neuronal development and inhibition of neuronal differentiation via Notch [208] | ||||
| S100B | C | VIP | 74 | 5192 | Astrocyte-derived cytokine; promotes neurite outgrowth; increases intracellular calcium in hippocampal neurons [155] | ||||
| GUSBL2 | C | VIP | 78 | 4968 | Aliase: GUSBP4. Glucuronidase beta pseudogene 4 (Gene ID: 375513) | ||||
| BMPR2 | C | VIP | 72 | 4907 | Bone morphogenetic protein receptor 2; involved in astrocyte development and survival/differentiation of GABAergic and dopaminergic neurons [165] | ||||
| MBNL1 | C | VIP | 62 | 4837 | Regulatory splicing factor involved in the splicing of the microtubule-associated protein Tau [169] | ||||
| MANBA | C | VIP | 68 | 4764 | Glycosyl hydrolase 2 family (Gene ID: 4126) | ||||
| RSC1A1 | C | VIP | 55 | 4723 | Regulates neuronal expression of the Na+-D-glucose cotransporter SGLT1; increased in the hippocampus during epileptic seizures [172] | ||||
| FGF7 | C | VIP | 61 | 4568 | Fibroblast growth factor 7; essential for inhibitory synapse formation in the hippocampus [173] | ||||
| DFFB | C | High-hub | 444 | 5575 | Aliase: DFF40. Triggering of DNA fragmentation, an early event in apoptotic neuronal cell death after brain injury [175, 176] | ||||
| LARP4 | C | High-hub | 311 | 5039 | La-related protein 4; interacts with poly(A)-binding protein and promotes mRNA homeostasis [177] | ||||
| EIF1 | C | High-hub | 257 | 3987 | Eukaryotic translation initiation factor 1 [178] | ||||
| PTPRZ1 | C | High-hub | 291 | 3935 | Receptor-type protein tyrosine phosphatase; it's concentration is increased in the hippocampus of MTLE patients [174] | ||||
| G3BP2 | D | Hub | 269 | 3168 | Ras-GTPase activating protein; contributes to stress granule formation [180]; expression levels altered in TLE [181] | ||||
| FTSJ1 | D | Hub | 268 | 3447 | RNA methyltransferase expressed in the hippocampus; associated to seizures [182] | ||||
| RMND5B | F | Hub | 297 | 2551 | Aliase: GID2. E3 ubiquitin ligase involved in the catabolic-induced degradation of gluconeogenic enzymes [157] | ||||
| TSEN2 | F | VIP | 87 | 5225 | tRNA splicing endonuclease complex subunit; associated with seizures [159] | ||||
| SLC6A1 | F | VIP | 95 | 4821 | Aliase: GAT1. GABA transporter 1; a major GABA transporter in the brain [156]; hippocampal expression increased in TLE patients [153] | ||||
| TTL | G | High-hub | 287 | 4647 | Tubulin-tyrosine-ligase; involved in neuronal organization and control of neurite extensions [184] | ||||
| PPFIBP1 | G | High-hub | 255 | 4425 | Liprin-family scaffold protein regulating cell adhesion, cell migration and synapse development [185] | ||||
1Community
2 Node Category