Table 1.
Genes that change differently on each side of the brain
| Gene symbol | Entrez gene name | TBI-I fold change | TBI-C fold change | TBI-I/TBI-C ratio | Molecular type |
|---|---|---|---|---|---|
| Extracellular Space | |||||
| SPP1 | secreted phosphoprotein 1 | 37.905 | 2.370 | 15.994 | cytokine |
| TIMP1 | TIMP metallopeptidase inhibitor 1 | 38.486 | 2.101 | 18.318 | cytokine |
| CP | ceruloplasmin (ferroxidase) | 27.838 | 8.477 | 3.284 | enzyme |
| FGL2 | fibrinogen-like 2 | 16.793 | 4.017 | 4.180 | peptidase |
| LCN2 | lipocalin 2 | 71.824 | 3.895 | 18.440 | transporter |
| SERPINA3 | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 58.488 | 2.509 | 23.311 | other |
| Plasma Membrane | |||||
| CD44 | CD44 molecule (Indian blood group) | 15.558 | 2.399 | 6.485 | enzyme |
| EHD4 | EH-domain containing 4 | 2.361 | −2.056 | 4.854 | enzyme |
| SDC1 | syndecan 1 | 13.681 | 2.566 | 5.332 | enzyme |
| KCND2 | potassium voltage-gated channel, Shal-related subfamily, member 2 | −2.792 | −7.585 | 2.717 | ion channel |
| KCNN4 | potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 | 3.088 | −9.429 | 29.117 | ion channel |
| CAMK2N1 | calcium/calmodulin-dependent protein kinase II inhibitor 1 | −11.813 | −23.824 | 2.017 | kinase |
| EGFR | epidermal growth factor receptor | 6.773 | 2.374 | 2.853 | kinase |
| PTPRF | protein tyrosine phosphatase, receptor type, F | −6.365 | −20.492 | 3.219 | phosphatase |
| IL6ST | interleukin 6 signal transducer | 2.307 | −3.283 | 7.574 | transmembrane receptor |
| CD68 | CD68 molecule | 4.365 | 2.007 | 2.175 | other |
| HLA-A | major histocompatibility complex, class I, A | 9.296 | 3.657 | 2.542 | other |
| PMEPA1 | prostate transmembrane protein, androgen induced 1 | 2.682 | −2.937 | 7.877 | other |
| Cytoplasm | |||||
| CYP1B1 | cytochrome P450, family 1, subfamily B, polypeptide 1 | 10.998 | 4.808 | 2.287 | enzyme |
| KIF3A | kinesin family member 3A | −5.083 | −11.754 | 2.312 | enzyme |
| MX1 | MX dynamin-like GTPase 1 | 28.177 | 7.326 | 3.846 | enzyme |
| PDE4B | phosphodiesterase 4B, cAMP-specific | 5.602 | 2.359 | 2.375 | enzyme |
| RND3 | Rho family GTPase 3 | 2.864 | −2.971 | 8.509 | enzyme |
| SRXN1 | sulfiredoxin 1 | 6.306 | 2.402 | 2.625 | enzyme |
| CARD11 | caspase recruitment domain family, member 11 | 7.343 | 2.892 | 2.539 | kinase |
| CSNK2A1 | casein kinase 2, alpha 1 polypeptide | 2.992 | −2.750 | 8.228 | kinase |
| EIF5B | eukaryotic translation initiation factor 5B | −3.044 | −8.766 | 2.880 | translation regulator |
| RASA1 | RAS p21 protein activator (GTPase activating protein) 1 | 2.392 | −2.105 | 5.035 | transporter |
| AHI1 | Abelson helper integration site 1 | 2.243 | −2.897 | 6.498 | other |
| CISD2 | CDGSH iron sulfur domain 2 | −7.833 | −19.012 | 2.427 | other |
| CMIP | c-Maf inducing protein | −3.778 | −13.763 | 3.643 | other |
| Ctdspl | CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like | −7.271 | −36.886 | 5.073 | other |
| HSPB1 | heat shock 27 kDa protein 1 | 46.922 | 2.639 | 17.780 | other |
| KIFAP3 | kinesin-associated protein 3 | −2.281 | −7.831 | 3.433 | other |
| LCP1 | lymphocyte cytosolic protein 1 (L-plastin) | 6.082 | 2.799 | 2.173 | other |
| LSP1 | lymphocyte-specific protein 1 | 11.716 | 2.140 | 5.475 | other |
| PHLDA1 | pleckstrin homology-like domain, family A, member 1 | 5.129 | 2.160 | 2.375 | other |
| RDX | radixin | 4.828 | −5.274 | 25.463 | other |
| Slpi | secretory leukocyte peptidase inhibitor | 82.908 | 3.119 | 26.582 | other |
| Tpm3 | tropomyosin 3 | 2.592 | −2.715 | 7.037 | other |
| TRIM54 | tripartite motif containing 54 | −4.426 | −2.032 | −2.178 | other |
| Nucleus | |||||
| SETD8 | SET domain containing (lysine methyltransferase) 8 | 2.029 | −3.930 | 7.974 | enzyme |
| TOP2A | topoisomerase (DNA) II alpha 170 kDa | 2.260 | −2.406 | 5.438 | enzyme |
| CDK11A | cyclin-dependent kinase 11A | −4.290 | −14.872 | 3.467 | kinase |
| GSK3B | glycogen synthase kinase 3 beta | −2.733 | −6.635 | 2.428 | kinase |
| SRPK2 | SRSF protein kinase 2 | −5.614 | −23.589 | 4.202 | kinase |
| THRA | thyroid hormone receptor, alpha | −2.799 | −11.518 | 4.115 | ligand-dependent nuclear receptor |
| ATRX | alpha thalassemia/mental retardation syndrome X-linked | 2.091 | −5.964 | 12.471 | transcription regulator |
| BTG2 | BTG family, member 2 | −2.220 | −5.803 | 2.614 | transcription regulator |
| CCAR1 | cell division cycle and apoptosis regulator 1 | −2.943 | −11.648 | 3.958 | transcription regulator |
| CCND1 | cyclin D1 | 2.152 | −2.027 | 4.362 | transcription regulator |
| CEBPD | CCAAT/enhancer binding protein (C/EBP), delta | 11.271 | 2.037 | 5.533 | transcription regulator |
| DEK | DEK proto-oncogene | −3.006 | −7.352 | 2.446 | transcription regulator |
| DNAJB6 | DnaJ (Hsp40) homolog, subfamily B, member 6 | −4.383 | 5.614 | −24.606 | transcription regulator |
| KLF13 | Kruppel-like factor 13 | −2.006 | −4.582 | 2.284 | transcription regulator |
| KLF6 | Kruppel-like factor 6 | 6.003 | 2.865 | 2.095 | transcription regulator |
| NAA15 | N(alpha)-acetyltransferase 15, NatA auxiliary subunit | 3.605 | −3.751 | 13.522 | transcription regulator |
| NFIX | nuclear factor I/X (CCAAT-binding transcription factor) | −2.548 | −8.112 | 3.184 | transcription regulator |
| PA2G4 | proliferation-associated 2G4, 38 kDa | −2.702 | −5.783 | 2.140 | transcription regulator |
| SMARCA4 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 | 2.521 | −7.712 | 19.442 | transcription regulator |
| STAT3 | signal transducer and activator of transcription 3 (acute-phase response factor) | 4.219 | −3.771 | 15.910 | transcription regulator |
| TBL1XR1 | transducin (beta)-like 1 X-linked receptor 1 | 2.587 | −2.134 | 5.521 | transcription regulator |
| TCF4 | transcription factor 4 | −2.216 | −4.625 | 2.087 | transcription regulator |
| TPR | translocated promoter region, nuclear basket protein | 2.212 | −2.728 | 6.034 | transporter |
| Brd4 | bromodomain containing 4 | −3.528 | −15.202 | 4.309 | other |
| CDT1 | chromatin licensing and DNA replication factor 1 | 3.098 | −2.295 | 7.110 | other |
| GADD45G | growth arrest and DNA-damage-inducible, gamma | 3.191 | −2.384 | 7.607 | other |
| PSIP1 | PC4 and SFRS1 interacting protein 1 | −2.663 | 2.113 | −5.627 | other |
| Rbm25 | RNA binding motif protein 25 | −5.547 | −16.213 | 2.923 | other |
| THOC2 | THO complex 2 | 2.119 | −4.886 | 10.353 | other |
| Unknown | |||||
| EIF3C | eukaryotic translation initiation factor 3, subunit C | −4.369 | −9.072 | 2.076 | translation regulator |
| Nos1ap | nitric oxide synthase 1 (neuronal) adaptor protein | −2.698 | −5.717 | 2.119 | other |
| RASSF4 | Ras association (RalGDS/AF-6) domain family member 4 | 4.289 | 2.106 | 2.037 | other |
TBI-I/TBI-C Ratio: Gene increased on both sides (TBI-I > TBI-C): ratio = (TBI-I)/(TBI-C); Gene decreased on both sides (TBI-I > TBI-C): ratio = 1/[(TBI-I)/(TBI-C)]; Gene decreased on both sides (TBI-I < TBI-C): ratio = −1/[(TBI-C)/(TBI-I)]; Gene increased ipsilaterally and decreased contralaterally: ratio = (TBI-I)/-[1/(TBI-C)]; Gene decreased ipsilaterally and increased contralaterally: ratio = (TBI-C)/[1/(TBI-I)]