Table 6.
TBI-I Gene interaction hierarchy (GIH)
| Gene symbol | Entrez gene name | Fold change | Cellular compartment | Molecular type |
|---|---|---|---|---|
| Primary | ||||
| ATF3 | activating transcription factor 3 | 12.027 | Nucleus | transcription regulator |
| CCND1 | cyclin D1 | 2.152 | Nucleus | transcription regulator |
| CEBPB | CCAAT/enhancer binding protein (C/EBP), beta | 3.366 | Nucleus | transcription regulator |
| CREB1 | cAMP responsive element binding protein 1 | 2.666 | Nucleus | transcription regulator |
| CREBBP | CREB binding protein | 2.421 | Nucleus | transcription regulator |
| MDM2 | MDM2 proto-oncogene, E3 ubiquitin protein ligase | 2.01 | Nucleus | transcription regulator |
| NFE2L2 | nuclear factor, erythroid 2-like 2 | 2.452 | Nucleus | transcription regulator |
| SMARCA4 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 | 2.521 | Nucleus | transcription regulator |
| STAT3 | signal transducer and activator of transcription 3 (acute-phase response factor) | 4.219 | Nucleus | transcription regulator |
| CDK1 | cyclin-dependent kinase 1 | 2.105 | Nucleus | kinase |
| CSNK2A1 | casein kinase 2, alpha 1 polypeptide | 2.992 | Cytoplasm | kinase |
| EGFR | epidermal growth factor receptor | 6.773 | Plasma Membrane | kinase |
| GSK3B | glycogen synthase kinase 3 beta | −2.733 | Nucleus | kinase |
| CD44 | CD44 molecule (Indian blood group) | 15.558 | Plasma Membrane | enzyme |
| FN1 | fibronectin 1 | 3.97 | Extracellular Space | enzyme |
| TRAF6 | TNF receptor-associated factor 6, E3 ubiquitin protein ligase | 2.163 | Cytoplasm | enzyme |
| CASP3 | caspase 3, apoptosis-related cysteine peptidase | 2.535 | Cytoplasm | peptidase |
| ELAVL1 | ELAV like RNA binding protein 1 | 3.275 | Cytoplasm | other |
| Secondary | ||||
| CEBPD | CCAAT/enhancer binding protein (C/EBP), delta | 11.271 | Nucleus | transcription regulator |
| CREM | cAMP responsive element modulator | 2.165 | Nucleus | transcription regulator |
| EGR2 | early growth response 2 | 2.271 | Nucleus | transcription regulator |
| FOSL1 | FOS-like antigen 1 | 5.875 | Nucleus | transcription regulator |
| KLF4 | Kruppel-like factor 4 (gut) | 2.057 | Nucleus | transcription regulator |
| MITF | microphthalmia-associated transcription factor | 4.755 | Nucleus | transcription regulator |
| TCF4 | transcription factor 4 | −2.216 | Nucleus | transcription regulator |
| HSPA1A/HSPA1B | heat shock 70 kDa protein 1A | 3.137 | Cytoplasm | enzyme |
| MCM2 | minichromosome maintenance complex component 2 | 2.57 | Nucleus | enzyme |
| PTGS2 | prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) | 3.106 | Cytoplasm | enzyme |
| IL1B | interleukin 1, beta | 5.166 | Extracellular Space | cytokine |
| SPP1 | secreted phosphoprotein 1 | 37.905 | Extracellular Space | cytokine |
| CDKN1B | cyclin-dependent kinase inhibitor 1B (p27, Kip1) | 3.732 | Nucleus | kinase |
| IKBKB | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta | 2.127 | Cytoplasm | kinase |
| KPNB1 | karyopherin (importin) beta 1 | 3.173 | Nucleus | transporter |
| MCL1 | myeloid cell leukemia 1 | 3.25 | Cytoplasm | transporter |
| THRA | thyroid hormone receptor, alpha | −2.799 | Nucleus | ligand-dependent nuclear receptor |
| CASP7 | caspase 7, apoptosis-related cysteine peptidase | 2.579 | Cytoplasm | peptidase |
| BAG3 | BCL2-associated athanogene 3 | 4.045 | Cytoplasm | other |
| CCNA2 | cyclin A2 | 2.633 | Nucleus | other |
| GFAP | glial fibrillary acidic protein | 3.011 | Cytoplasm | other |
| HSPA9 | heat shock 70 kDa protein 9 (mortalin) | 2.666 | Cytoplasm | other |
| HSPB1 | heat shock 27 kDa protein 1 | 46.922 | Cytoplasm | other |
| SNCA | synuclein, alpha (non A4 component of amyloid precursor) | −2.169 | Cytoplasm | other |
| Peripheral | ||||
| ACSL5 | acyl-CoA synthetase long-chain family member 5 | −2.361 | Cytoplasm | enzyme |
| ANXA1 | annexin A1 | 3.535 | Plasma Membrane | enzyme |
| CHSY1 | chondroitin sulfate synthase 1 | 2.873 | Cytoplasm | enzyme |
| CP | ceruloplasmin (ferroxidase) | 27.838 | Extracellular Space | enzyme |
| EHD4 | EH-domain containing 4 | 2.361 | Plasma Membrane | enzyme |
| GCLM | glutamate-cysteine ligase, modifier subunit | 2.019 | Cytoplasm | enzyme |
| HMOX1 | heme oxygenase (decycling) 1 | 9.778 | Cytoplasm | enzyme |
| MCM8 | minichromosome maintenance complex component 8 | 2.027 | Nucleus | enzyme |
| MX1 | MX dynamin-like GTPase 1 | 28.177 | Cytoplasm | enzyme |
| PDE4B | phosphodiesterase 4B, cAMP-specific | 5.602 | Cytoplasm | enzyme |
| RAB35 | RAB35, member RAS oncogene family | 2.086 | Cytoplasm | enzyme |
| RRM2 | ribonucleotide reductase M2 | 3.34 | Nucleus | enzyme |
| SDC1 | syndecan 1 | 13.681 | Plasma Membrane | enzyme |
| SETD8 | SET domain containing (lysine methyltransferase) 8 | 2.029 | Nucleus | enzyme |
| SGPL1 | sphingosine-1-phosphate lyase 1 | 3.108 | Cytoplasm | enzyme |
| SRXN1 | sulfiredoxin 1 | 6.306 | Cytoplasm | enzyme |
| TGM2 | transglutaminase 2 | 3.574 | Cytoplasm | enzyme |
| TOP2A | topoisomerase (DNA) II alpha 170 kDa | 2.26 | Nucleus | enzyme |
| BCL11A | B-cell CLL/lymphoma 11A (zinc finger protein) | −2.38 | Nucleus | transcription regulator |
| BTG2 | BTG family, member 2 | −2.22 | Nucleus | transcription regulator |
| CCAR1 | cell division cycle and apoptosis regulator 1 | −2.943 | Nucleus | transcription regulator |
| CSRNP1 | cysteine-serine-rich nuclear protein 1 | 2.821 | Nucleus | transcription regulator |
| DEK | DEK proto-oncogene | −3.006 | Nucleus | transcription regulator |
| DNAJB6 | DnaJ (Hsp40) homolog, subfamily B, member 6 | −4.383 | Nucleus | transcription regulator |
| ETV5 | ets variant 5 | −2.163 | Nucleus | transcription regulator |
| KLF13 | Kruppel-like factor 13 | −2.006 | Nucleus | transcription regulator |
| KLF6 | Kruppel-like factor 6 | 6.003 | Nucleus | transcription regulator |
| NAA15 | N(alpha)-acetyltransferase 15, NatA auxiliary subunit | 3.605 | Nucleus | transcription regulator |
| NFIX | nuclear factor I/X (CCAAT-binding transcription factor) | −2.548 | Nucleus | transcription regulator |
| NFKB2 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | 2.768 | Nucleus | transcription regulator |
| PA2G4 | proliferation-associated 2G4, 38 kDa | −2.702 | Nucleus | transcription regulator |
| PRDM2 | PR domain containing 2, with ZNF domain | 3.677 | Nucleus | transcription regulator |
| TBL1XR1 | transducin (beta)-like 1 X-linked receptor 1 | 2.587 | Nucleus | transcription regulator |
| TCEB3 | transcription elongation factor B (SIII), polypeptide 3 (110 kDa, elongin A) | 3.053 | Nucleus | transcription regulator |
| CAMK1G | calcium/calmodulin-dependent protein kinase IG | −2.271 | Cytoplasm | kinase |
| CAMK2N1 | calcium/calmodulin-dependent protein kinase II inhibitor 1 | −11.813 | Plasma Membrane | kinase |
| CARD11 | caspase recruitment domain family, member 11 | 7.343 | Cytoplasm | kinase |
| CDK11A | cyclin-dependent kinase 11A | −4.29 | Nucleus | kinase |
| FGR | FGR proto-oncogene, Src family tyrosine kinase | 3.915 | Nucleus | kinase |
| HCK | HCK proto-oncogene, Src family tyrosine kinase | 3.887 | Cytoplasm | kinase |
| HSPB8 | heat shock 22 kDa protein 8 | 4.112 | Cytoplasm | kinase |
| LATS1 | large tumor suppressor kinase 1 | 2.003 | Nucleus | kinase |
| MAP4K4 | mitogen-activated protein kinase kinase kinase kinase 4 | 2.258 | Cytoplasm | kinase |
| NEK6 | NIMA-related kinase 6 | 2.322 | Nucleus | kinase |
| SRPK2 | SRSF protein kinase 2 | −5.614 | Nucleus | kinase |
| TJP2 | tight junction protein 2 | 2.552 | Plasma Membrane | kinase |
| Ccl2 | chemokine (C-C motif) ligand 2 | 195.455 | Extracellular Space | cytokine |
| CCL3L3 | chemokine (C-C motif) ligand 3-like 3 | 5.269 | Extracellular Space | cytokine |
| CCL4 | chemokine (C-C motif) ligand 4 | 2.162 | Extracellular Space | cytokine |
| Ccl6 | chemokine (C-C motif) ligand 6 | 10.291 | Extracellular Space | cytokine |
| Ccl7 | chemokine (C-C motif) ligand 7 | 124.78 | Extracellular Space | cytokine |
| CXCL3 | chemokine (C-X-C motif) ligand 3 | 13.211 | Extracellular Space | cytokine |
| Cxcl9 | chemokine (C-X-C motif) ligand 9 | 2.846 | Extracellular Space | cytokine |
| TIMP1 | TIMP metallopeptidase inhibitor 1 | 38.486 | Extracellular Space | cytokine |
| IL6R | interleukin 6 receptor | 2.315 | Plasma Membrane | transmembrane receptor |
| IL6ST | interleukin 6 signal transducer | 2.307 | Plasma Membrane | transmembrane receptor |
| ITGB2 | integrin, beta 2 (complement component 3 receptor 3 and 4 subunit) | 2.675 | Plasma Membrane | transmembrane receptor |
| TLR4 | toll-like receptor 4 | 2.699 | Plasma Membrane | transmembrane receptor |
| TNFRSF1A | tumor necrosis factor receptor superfamily, member 1A | 3.555 | Plasma Membrane | transmembrane receptor |
| UNC5B | unc-5 homolog B (C. elegans) | 2.067 | Plasma Membrane | transmembrane receptor |
| ALB | albumin | −3.125 | Extracellular Space | transporter |
| LCN2 | lipocalin 2 | 71.824 | Extracellular Space | transporter |
| RASA1 | RAS p21 protein activator (GTPase activating protein) 1 | 2.392 | Cytoplasm | transporter |
| TPR | translocated promoter region, nuclear basket protein | 2.212 | Nucleus | transporter |
| FGL2 | fibrinogen-like 2 | 16.793 | Extracellular Space | peptidase |
| SENP2 | SUMO1/sentrin/SMT3 specific peptidase 2 | 2.051 | Nucleus | peptidase |
| DUSP5 | dual specificity phosphatase 5 | 3.285 | Nucleus | phosphatase |
| PTPRF | protein tyrosine phosphatase, receptor type, F | −6.365 | Plasma Membrane | phosphatase |
| EIF3C | eukaryotic translation initiation factor 3, subunit C | −4.369 | Other | translation regulator |
| EIF5B | eukaryotic translation initiation factor 5B | −3.044 | Cytoplasm | translation regulator |
| FGF2 | fibroblast growth factor 2 (basic) | 2.387 | Extracellular Space | growth factor |
| KCND2 | potassium voltage-gated channel, Shal-related subfamily, member 2 | −2.792 | Plasma Membrane | ion channel |
| AHI1 | Abelson helper integration site 1 | 2.243 | Cytoplasm | other |
| BCL2A1 | BCL2-related protein A1 | 3.055 | Cytoplasm | other |
| CALB1 | calbindin 1, 28 kDa | −2.091 | Cytoplasm | other |
| CD68 | CD68 molecule | 4.365 | Plasma Membrane | other |
| CDCA7L | cell division cycle associated 7-like | 2.648 | Nucleus | other |
| CDT1 | chromatin licensing and DNA replication factor 1 | 3.098 | Nucleus | other |
| CISD2 | CDGSH iron sulfur domain 2 | −7.833 | Cytoplasm | other |
| CMIP | c-Maf inducing protein | −3.778 | Cytoplasm | other |
| DAB2 | Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila) | 3.053 | Plasma Membrane | other |
| DES | desmin | 2.857 | Cytoplasm | other |
| DNAJB9 | DnaJ (Hsp40) homolog, subfamily B, member 9 | 2.128 | Nucleus | other |
| FLNA | filamin A, alpha | 3.45 | Cytoplasm | other |
| GADD45G | growth arrest and DNA-damage-inducible, gamma | 3.191 | Nucleus | other |
| HLA-A | major histocompatibility complex, class I, A | 9.296 | Plasma Membrane | other |
| HSPA2 | heat shock 70 kDa protein 2 | 3.51 | Cytoplasm | other |
| LCP1 | lymphocyte cytosolic protein 1 (L-plastin) | 6.082 | Cytoplasm | other |
| LSP1 | lymphocyte-specific protein 1 | 11.716 | Cytoplasm | other |
| MMS22L | MMS22-like, DNA repair protein | 2.918 | Nucleus | other |
| MSI2 | musashi RNA-binding protein 2 | 2.288 | Cytoplasm | other |
| PDLIM7 | PDZ and LIM domain 7 (enigma) | 4.695 | Cytoplasm | other |
| PHLDA1 | pleckstrin homology-like domain, family A, member 1 | 5.129 | Cytoplasm | other |
| PMEPA1 | prostate transmembrane protein, androgen induced 1 | 2.682 | Plasma Membrane | other |
| PSIP1 | PC4 and SFRS1 interacting protein 1 | −2.663 | Nucleus | other |
| RDX | radixin | 4.828 | Cytoplasm | other |
| SERPINA3 | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 58.488 | Extracellular Space | other |
| SPIN1 | spindlin 1 | 2.178 | Nucleus | other |
| SUDS3 | suppressor of defective silencing 3 homolog (S. cerevisiae) | 2.228 | Nucleus | other |
| TAGLN2 | transgelin 2 | 3.891 | Cytoplasm | other |
| THOC2 | THO complex 2 | 2.119 | Nucleus | other |
| TMEM109 | transmembrane protein 109 | 2.106 | Cytoplasm | other |
| TMEM123 | transmembrane protein 123 | 2.348 | Plasma Membrane | other |
| Orphan | ||||
| CYP1B1 | cytochrome P450, family 1, subfamily B, polypeptide 1 | 10.998 | Cytoplasm | enzyme |
| KIF3A | kinesin family member 3A | −5.083 | Cytoplasm | enzyme |
| PTGR1 | prostaglandin reductase 1 | 2.258 | Cytoplasm | enzyme |
| RND3 | Rho family GTPase 3 | 2.864 | Cytoplasm | enzyme |
| WFS1 | Wolfram syndrome 1 (wolframin) | 2.083 | Cytoplasm | enzyme |
| ITPR2 | inositol 1,4,5-trisphosphate receptor, type 2 | 2.489 | Cytoplasm | ion channel |
| KCNN4 | potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 | 3.088 | Plasma Membrane | ion channel |
| ATRX | alpha thalassemia/mental retardation syndrome X-linked | 2.091 | Nucleus | transcription regulator |
| RAI14 | retinoic acid induced 14 | 3.284 | Nucleus | transcription regulator |
| CX3CL1 | chemokine (C-X3-C motif) ligand 1 | −2.044 | Extracellular Space | cytokine |
| PTGER3 | prostaglandin E receptor 3 (subtype EP3) | 2.425 | Plasma Membrane | G-protein coupled receptor |
| PI4K2A | phosphatidylinositol 4-kinase type 2 alpha | 2.96 | Cytoplasm | kinase |
| CD36 | CD36 molecule (thrombospondin receptor) | 5.08 | Plasma Membrane | transmembrane receptor |
| ARL11 | ADP-ribosylation factor-like 11 | 3.143 | Other | other |
| Brd4 | bromodomain containing 4 | −3.528 | Nucleus | other |
| CLN5 | ceroid-lipofuscinosis, neuronal 5 | 2.041 | Cytoplasm | other |
| Ctdspl | CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like | −7.271 | Cytoplasm | other |
| KIFAP3 | kinesin-associated protein 3 | −2.281 | Cytoplasm | other |
| Nos1ap | nitric oxide synthase 1 (neuronal) adaptor protein | −2.698 | Other | other |
| PCDH15 | protocadherin-related 15 | 2.147 | Plasma Membrane | other |
| RASSF4 | Ras association (RalGDS/AF-6) domain family member 4 | 4.289 | Other | other |
| Rbm25 | RNA binding motif protein 25 | −5.547 | Nucleus | other |
| Slpi | secretory leukocyte peptidase inhibitor | 82.908 | Cytoplasm | other |
| Tpm3 | tropomyosin 3 | 2.592 | Cytoplasm | other |
| TRIM54 | tripartite motif containing 54 | −4.426 | Cytoplasm | other |
Primary: >14 connections in GOI network (see text); Secondary: 8–14 connections in GOI network; Peripheral: <8 connections in GOI network; Orphan: No connections in GOI network; Italics= > Gene changes on both sides of the brain