Table 7 TBI-C Gene interaction hierarchy (GIH)
Gene symbol | Entrez gene name | Fold change | Cellular compartment | Molecular type |
|---|---|---|---|---|
Primary | Â | Â | Â | Â |
  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 | Â | Â | Â | Â |
 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 | Â | Â | Â | Â |
  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 | Â | Â | Â | Â |
 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 |