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Table 1 Genes that change differently on each side of the brain

From: Bilateral gene interaction hierarchy analysis of the cell death gene response emphasizes the significance of cell cycle genes following unilateral traumatic brain injury

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
  1. 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)]