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Table 7 TBI-C 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
Primary     
CCND1 cyclin D1 −2.027 Nucleus transcription regulator
 MED1 mediator complex subunit 1 −4.011 Nucleus transcription regulator
SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 −7.712 Nucleus transcription regulator
 SOX2 SRY (sex determining region Y)-box 2 −4.791 Nucleus transcription regulator
 SP1 Sp1 transcription factor −2.076 Nucleus transcription regulator
STAT3 signal transducer and activator of transcription 3 (acute-phase response factor) −3.771 Nucleus transcription regulator
CSNK2A1 casein kinase 2, alpha 1 polypeptide −2.75 Cytoplasm kinase
EGFR epidermal growth factor receptor 2.374 Plasma Membrane kinase
GSK3B glycogen synthase kinase 3 beta −6.635 Nucleus kinase
CD44 CD44 molecule (Indian blood group) 2.399 Plasma Membrane enzyme
HSP90AA1 heat shock protein 90 kDa alpha (cytosolic), class A member 1 −4.843 Cytoplasm enzyme
Secondary     
 FOXO1 forkhead box O1 −3.329 Nucleus transcription regulator
 MEF2A myocyte enhancer factor 2A −6.31 Nucleus transcription regulator
NFIX nuclear factor I/X (CCAAT-binding transcription factor) −8.112 Nucleus transcription regulator
TCF4 transcription factor 4 −4.625 Nucleus transcription regulator
 MAPK8 mitogen-activated protein kinase 8 2.102 Cytoplasm kinase
 PIK3R2 phosphoinositide-3-kinase, regulatory subunit 2 (beta) 2.332 Cytoplasm kinase
 PTK2B protein tyrosine kinase 2 beta 2.15 Cytoplasm kinase
 KRAS Kirsten rat sarcoma viral oncogene homolog −2.027 Cytoplasm enzyme
TOP2A topoisomerase (DNA) II alpha 170 kDa −2.406 Nucleus enzyme
 ATP2A2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 −2.607 Cytoplasm transporter
 BAX BCL2-associated X protein −3.306 Cytoplasm transporter
SPP1 secreted phosphoprotein 1 2.37 Extracellular Space cytokine
THRA thyroid hormone receptor, alpha −11.518 Nucleus ligand-dependent nuclear receptor
 TUFM Tu translation elongation factor, mitochondrial −2.109 Cytoplasm translation regulator
 CCND2 cyclin D2 −3.617 Nucleus other
HSPB1 heat shock 27 kDa protein 1 2.639 Cytoplasm other
Peripheral     
BTG2 BTG family, member 2 −5.803 Nucleus transcription regulator
CCAR1 cell division cycle and apoptosis regulator 1 −11.648 Nucleus transcription regulator
CEBPD CCAAT/enhancer binding protein (C/EBP), delta 2.037 Nucleus transcription regulator
DEK DEK proto-oncogene −7.352 Nucleus transcription regulator
DNAJB6 DnaJ (Hsp40) homolog, subfamily B, member 6 5.614 Nucleus transcription regulator
 GBX2 gastrulation brain homeobox 2 2.59 Nucleus transcription regulator
KLF6 Kruppel-like factor 6 2.865 Nucleus transcription regulator
 MAFG v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G −2.632 Nucleus transcription regulator
 MTDH metadherin −2.544 Cytoplasm transcription regulator
PA2G4 proliferation-associated 2G4, 38 kDa −5.783 Nucleus transcription regulator
 RSF1 remodeling and spacing factor 1 −2.618 Nucleus transcription regulator
TBL1XR1 transducin (beta)-like 1 X-linked receptor 1 −2.134 Nucleus transcription regulator
ZMYND11 zinc finger, MYND-type containing 11 −2.211 Nucleus transcription regulator
 ZNF148 zinc finger protein 148 2.114 Nucleus transcription regulator
 ACIN1 apoptotic chromatin condensation inducer 1 −2.515 Nucleus enzyme
CYP1B1 cytochrome P450, family 1, subfamily B, polypeptide 1 4.808 Cytoplasm enzyme
 DPYD dihydropyrimidine dehydrogenase 2.292 Cytoplasm enzyme
 MFN1 mitofusin 1 2.304 Cytoplasm enzyme
MX1 MX dynamin-like GTPase 1 7.326 Cytoplasm enzyme
SETD8 SET domain containing (lysine methyltransferase) 8 −3.93 Nucleus enzyme
 TTLL1 tubulin tyrosine ligase-like family, member 1 2.284 Extracellular Space enzyme
ACVR1C activin A receptor, type IC −9.107 Plasma Membrane kinase
CARD11 caspase recruitment domain family, member 11 2.892 Cytoplasm kinase
CDK11A cyclin-dependent kinase 11A −14.872 Nucleus kinase
 CDK19 cyclin-dependent kinase 19 −2.191 Nucleus kinase
 PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta −2.113 Cytoplasm kinase
 PRKAA2 protein kinase, AMP-activated, alpha 2 catalytic subunit −2.546 Cytoplasm kinase
SRPK2 SRSF protein kinase 2 −23.589 Nucleus kinase
 PPP3CB protein phosphatase 3, catalytic subunit, beta isozyme 2.1 Plasma Membrane phosphatase
PTPRF protein tyrosine phosphatase, receptor type, F −20.492 Plasma Membrane phosphatase
IL6ST interleukin 6 signal transducer −3.283 Plasma Membrane transmembrane receptor
 PRLR prolactin receptor −3.192 Plasma Membrane transmembrane receptor
LCN2 lipocalin 2 3.895 Extracellular Space transporter
RASA1 RAS p21 protein activator (GTPase activating protein) 1 −2.105 Cytoplasm transporter
TIMP1 TIMP metallopeptidase inhibitor 1 2.101 Extracellular Space cytokine
EIF5B eukaryotic translation initiation factor 5B −8.766 Cytoplasm translation regulator
AHI1 Abelson helper integration site 1 −2.897 Cytoplasm other
CDT1 chromatin licensing and DNA replication factor 1 −2.295 Nucleus other
CISD2 CDGSH iron sulfur domain 2 −19.012 Cytoplasm other
GADD45G growth arrest and DNA-damage-inducible, gamma −2.384 Nucleus other
HLA-A major histocompatibility complex, class I, A 3.657 Plasma Membrane other
 LINGO1 leucine rich repeat and Ig domain containing 1 −2.173 Plasma Membrane other
 MAFB v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B −2.018 Nucleus other
PHLDA1 pleckstrin homology-like domain, family A, member 1 2.16 Cytoplasm other
PMEPA1 prostate transmembrane protein, androgen induced 1 −2.937 Plasma Membrane other
PSIP1 PC4 and SFRS1 interacting protein 1 2.113 Nucleus other
 RAD23B RAD23 homolog B (S. cerevisiae) −2.217 Nucleus other
RASSF4 Ras association (RalGDS/AF-6) domain family member 4 2.106 Other other
RDX radixin −5.274 Cytoplasm other
 Serbp1 Serpine1 mRNA binding protein 1 −2.059 Cytoplasm other
SERPINA3 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 2.509 Extracellular Space other
Orphan     
 AURKAIP1 aurora kinase A interacting protein 1 −2.023 Nucleus enzyme
CP ceruloplasmin (ferroxidase) 8.477 Extracellular Space enzyme
EHD4 EH-domain containing 4 −2.056 Plasma Membrane enzyme
 ENTPD5 ectonucleoside triphosphate diphosphohydrolase 5 −2.055 Cytoplasm enzyme
KIF3A kinesin family member 3A −11.754 Cytoplasm enzyme
NDUFAB1 NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8 kDa −2.028 Cytoplasm enzyme
PDE4B phosphodiesterase 4B, cAMP-specific 2.359 Cytoplasm enzyme
RND3 Rho family GTPase 3 −2.971 Cytoplasm enzyme
SDC1 syndecan 1 2.566 Plasma Membrane enzyme
SRXN1 sulfiredoxin 1 2.402 Cytoplasm enzyme
ATRX alpha thalassemia/mental retardation syndrome X-linked −5.964 Nucleus transcription regulator
KLF13 Kruppel-like factor 13 −4.582 Nucleus transcription regulator
NAA15 N(alpha)-acetyltransferase 15, NatA auxiliary subunit −3.751 Nucleus transcription regulator
KCND2 potassium voltage-gated channel, Shal-related subfamily, member 2 −7.585 Plasma Membrane ion channel
KCNN4 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 −9.429 Plasma Membrane ion channel
CAMK2N1 calcium/calmodulin-dependent protein kinase II inhibitor 1 −23.824 Plasma Membrane kinase
 TRPM7 transient receptor potential cation channel, subfamily M, member 7 2.226 Plasma Membrane kinase
 ATP2B2 ATPase, Ca++ transporting, plasma membrane 2 2.276 Plasma Membrane transporter
TPR translocated promoter region, nuclear basket protein −2.728 Nucleus transporter
FGL2 fibrinogen-like 2 4.017 Extracellular Space peptidase
EIF3C eukaryotic translation initiation factor 3, subunit C −9.072 Other translation regulator
Brd4 bromodomain containing 4 −15.202 Nucleus other
CCDC86 coiled-coil domain containing 86 −2.149 Nucleus other
CD68 CD68 molecule 2.007 Plasma Membrane other
 CDH13 cadherin 13 −2.692 Plasma Membrane other
CMIP c-Maf inducing protein −13.763 Cytoplasm other
Ctdspl CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like −36.886 Cytoplasm other
KIFAP3 kinesin-associated protein 3 −7.831 Cytoplasm other
LCP1 lymphocyte cytosolic protein 1 (L-plastin) 2.799 Cytoplasm other
LSP1 lymphocyte-specific protein 1 2.14 Cytoplasm other
Nos1ap nitric oxide synthase 1 (neuronal) adaptor protein −5.717 Other other
 PALLD palladin, cytoskeletal associated protein −5.086 Plasma Membrane other
Rbm25 RNA binding motif protein 25 −16.213 Nucleus other
Slpi secretory leukocyte peptidase inhibitor 3.119 Cytoplasm other
THOC2 THO complex 2 −4.886 Nucleus other
Tpm3 tropomyosin 3 −2.715 Cytoplasm other
TRIM54 tripartite motif containing 54 −2.032 Cytoplasm other
  1. Primary: >8 connections in GOI network (see text); Secondary: 4–8 connections in GOI network; Peripheral: <4 connections in GOI network; Orphan: No connections in GOI network; Italics= > Gene changes on both sides of the brain