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Table 6 TBI-I Gene interaction hierarchy (GIH)

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 Fold change Cellular compartment Molecular type
 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
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
 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
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
  1. 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