Table 3 Gene interaction hierarchy (GIH)
Gene symbol | Entrez gene name | Fold change (TBI-I | TBI-C) | Cellular compartment | Molecular type |
|---|---|---|---|---|
Primary | Â | Â | Â | Â |
CEBPB | CCAAT/enhancer binding protein (C/EBP), beta | 3.37 | ~ | Nucleus | transcription regulator |
FOS | FBJ murine osteosarcoma viral oncogene homolog | 2.83 | ~ | Nucleus | transcription regulator |
IRF1 | interferon regulatory factor 1 | 2.22 | ~ | Nucleus | transcription regulator |
IRF7 | interferon regulatory factor 7 | 2.78 | ~ | Nucleus | transcription regulator |
MYC | v-myc myelocytomatosis viral oncogene homolog (avian) | 3.96 | ~ | Nucleus | transcription regulator |
NFKB2 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | 2.77 | ~ | Nucleus | transcription regulator |
STAT3 | signal transducer and activator of transcription 3 (acute-phase response factor) | 4.22 | -3.77 | Nucleus | transcription regulator |
EGFR | epidermal growth factor receptor | 6.77 | 2.37 | Plasma membrane | kinase |
IKBKB | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta | 2.13 | ~ | Cytoplasm | kinase |
JAK2 | Janus kinase 2 | 2.53 | ~ | Cytoplasm | kinase |
LYN | v-yes-1 Yamaguchi sarcoma viral related oncogene homolog | 6.94 | 3.78 | Cytoplasm | kinase |
FN1 | fibronectin 1 | 3.97 | ~ | Extracellular space | enzyme |
HSP90AA1 | heat shock protein 90 kDa alpha (cytosolic), class A member 1 | ~ | -4.84 | Cytoplasm | enzyme |
IL1B | interleukin 1, beta | 5.17 | ~ | Extracellular space | cytokine |
CASP3 | caspase 3, apoptosis-related cysteine peptidase | 2.54 | ~ | Cytoplasm | peptidase |
TLR4 | toll-like receptor 4 | 2.70 | ~ | Plasma membrane | transmembrane receptor |
CCND1 | cyclin D1 | 2.15 | -2.03 | Nucleus | other |
CD44 | CD44 molecule (Indian blood group) | 15.56 | 2.40 | Plasma membrane | other |
CDKN1A | cyclin-dependent kinase inhibitor 1A (p21, Cip1) | 2.68 | ~ | Nucleus | other |
MYD88 | myeloid differentiation primary response gene (88) | 2.70 | ~ | Plasma membrane | other |
Secondary | Â | Â | Â | Â |
ERAP1 | endoplasmic reticulum aminopeptidase 1 | 5.84 | 3.05 | Extracellular space | peptidase |
MMP13 | matrix metallopeptidase 13 (collagenase 3) | 2.26 | ~ | Extracellular space | peptidase |
MMP14 | matrix metallopeptidase 14 (membrane-inserted) | ~ | -3.03 | Extracellular space | peptidase |
MMP3 | matrix metallopeptidase 3 (stromelysin 1, progelatinase) | 4.05 | ~ | Extracellular space | peptidase |
MMP9 | matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase) | 7.18 | ~ | Extracellular space | peptidase |
PSMB8 | proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7) | 3.30 | ~ | Cytoplasm | peptidase |
PSMB9 | proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2) | 2.32 | ~ | Cytoplasm | peptidase |
ICAM1 | intercellular adhesion molecule 1 | 2.60 | ~ | Plasma membrane | transmembrane receptor |
IL6R | interleukin 6 receptor | 2.32 | ~ | Plasma membrane | transmembrane receptor |
IL6ST | interleukin 6 signal transducer (gp130, oncostatin M receptor) | 2.31 | -3.28 | Plasma membrane | transmembrane receptor |
TLR2 | toll-like receptor 2 | 2.33 | ~ | Plasma membrane | transmembrane receptor |
TNFRSF1A | tumor necrosis factor receptor superfamily, member 1A | 3.56 | ~ | Plasma membrane | transmembrane receptor |
CBL | Cas-Br-M (murine) ecotropic retroviral transforming sequence | -3.40 | -6.13 | Nucleus | transcription regulator |
CEBPD | CCAAT/enhancer binding protein (C/EBP), delta | 11.27 | 2.04 | Nucleus | transcription regulator |
IRF2 | interferon regulatory factor 2 | ~ | 2.17 | Nucleus | transcription regulator |
IRF9 | interferon regulatory factor 9 | 3.26 | ~ | Nucleus | transcription regulator |
CCL7 | chemokine (C-C motif) ligand 7 | 124.78 | ~ | Extracellular space | cytokine |
CXCL10 | chemokine (C-X-C motif) ligand 10 | ~ | -3.29 | Extracellular space | cytokine |
SPP1 | secreted phosphoprotein 1 | 37.91 | 2.37 | Extracellular space | cytokine |
AKT1 | v-akt murine thymoma viral oncogene homolog 1 | 2.04 | ~ | Cytoplasm | kinase |
BTK | Bruton agammaglobulinemia tyrosine kinase | 2.29 | ~ | Cytoplasm | kinase |
EIF2AK2 | eukaryotic translation initiation factor 2-alpha kinase 2 | 2.18 | ~ | Cytoplasm | kinase |
CCR5 | chemokine (C-C motif) receptor 5 | 2.09 | ~ | Plasma membrane | G-protein coupled receptor |
CXCR4 | chemokine (C-X-C motif) receptor 4 | 2.31 | ~ | Plasma membrane | G-protein coupled receptor |
HBEGF | heparin-binding EGF-like growth factor | 7.07 | ~ | Extracellular space | growth factor |
FGF2 | fibroblast growth factor 2 (basic) | 2.39 | ~ | Extracellular space | growth factor |
RORA | RAR-related orphan receptor A | 2.50 | ~ | Nucleus | ligand-dependent nuclear receptor |
THRA | thyroid hormone receptor, alpha | -2.80 | -11.52 | Nucleus | ligand-dependent nuclear receptor |
RAC1 | ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) | 2.32 | ~ | Plasma membrane | enzyme |
PTPN6 | protein tyrosine phosphatase, non-receptor type 6 | 3.64 | ~ | Cytoplasm | phosphatase |
HSPA1A/HSPA1B | heat shock 70 kDa protein 1A | 3.14 | ~ | Cytoplasm | other |
ITGA5 | integrin, alpha 5 (fibronectin receptor, alpha polypeptide) | 4.83 | 2.68 | Plasma membrane | other |
SDC1 | syndecan 1 | 13.68 | 2.57 | Plasma membrane | other |
TIMP1 | TIMP metallopeptidase inhibitor 1 | 38.49 | 2.10 | Extracellular space | other |
Peripheral | Â | Â | Â | Â |
CCL13/CCL2 | chemokine (C-C motif) ligand 13/2 | 195.46 | ~ | Extracellular space | cytokine |
CCL3L1/CCL3L3 | chemokine (C-C motif) ligand 3-like 1 | 5.27 | ~ | Extracellular space | cytokine |
CCL4 | chemokine (C-C motif) ligand 4 | 2.16 | ~ | Extracellular space | cytokine |
Ccl6 | chemokine (C-C motif) ligand 6 | 10.29 | ~ | Extracellular space | cytokine |
CSF1 | colony stimulating factor 1 (macrophage) | 3.70 | 2.09 | Extracellular space | cytokine |
CXCL13 | chemokine (C-X-C motif) ligand 13 | 3.78 | ~ | Extracellular space | cytokine |
CXCL14 | chemokine (C-X-C motif) ligand 14 | ~ | 2.13 | Extracellular space | cytokine |
CXCL9 | chemokine (C-X-C motif) ligand 9 | 2.85 | ~ | Extracellular space | cytokine |
CD14 | CD14 molecule | 10.66 | ~ | Plasma membrane | transmembrane receptor |
FCGR2B | Fc fragment of IgG, low affinity IIb, receptor (CD32) | 5.12 | ~ | Plasma membrane | transmembrane receptor |
HLA-C | major histocompatibility complex, class I, C | 9.30 | 3.66 | Plasma membrane | transmembrane receptor |
HLA-DRA | major histocompatibility complex, class II, DR alpha | 2.70 | ~ | Plasma membrane | transmembrane receptor |
IL13RA1 | interleukin 13 receptor, alpha 1 | 4.53 | 2.27 | Plasma membrane | transmembrane receptor |
IL1R2 | interleukin 1 receptor, type II | 37.03 | ~ | Plasma membrane | transmembrane receptor |
GBP2 (includes EG:14469) | guanylate binding protein 2, interferon-inducible | 9.13 | ~ | Cytoplasm | enzyme |
MX1 | myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) | 28.18 | 7.33 | Nucleus | enzyme |
RALBP1 | ralA binding protein 1 | 2.23 | ~ | Cytoplasm | enzyme |
TOP2A | topoisomerase (DNA) II alpha 170 kDa | 2.26 | -2.41 | Nucleus | enzyme |
EGR2 | early growth response 2 | 2.27 | ~ | Nucleus | transcription regulator |
NFE2L2 | nuclear factor (erythroid-derived 2)-like 2 | 2.45 | ~ | Nucleus | transcription regulator |
ZFP36 | zinc finger protein 36, C3H type, homolog (mouse) | 7.28 | ~ | Nucleus | transcription regulator |
ABCC1 | ATP-binding cassette, sub-family C (CFTR/MRP), member 1 | ~ | -3.11 | Plasma membrane | transporter |
LCN2 | lipocalin 2 | 71.82 | 3.90 | Extracellular space | transporter |
RASA1 | RAS p21 protein activator (GTPase activating protein) 1 | 2.39 | -2.11 | Cytoplasm | transporter |
NR1H2 | nuclear receptor subfamily 1, group H, member 2 | 2.15 | ~ | Nucleus | ligand-dependent nuclear receptor |
NR1H3 | nuclear receptor subfamily 1, group H, member 3 | 2.16 | ~ | Nucleus | ligand-dependent nuclear receptor |
HSPB8 | heat shock 22 kDa protein 8 | 4.11 | ~ | Cytoplasm | kinase |
RIPK3 | receptor-interacting serine-threonine kinase 3 | 7.55 | ~ | Plasma membrane | kinase |
CASP4 | caspase 4, apoptosis-related cysteine peptidase | 3.05 | ~ | Cytoplasm | peptidase |
DPP8 | dipeptidyl-peptidase 8 | ~ | 2.06 | Cytoplasm | peptidase |
ANGPT2 | angiopoietin 2 | 2.98 | ~ | Extracellular space | growth factor |
CD63 | CD63 molecule | 2.07 | ~ | Plasma membrane | other |
HSPB1 | heat shock 27 kDa protein 1 | 46.92 | 2.64 | Cytoplasm | other |
IER3 | immediate early response 3 | 2.35 | ~ | Cytoplasm | other |
IFI44 | interferon-induced protein 44 | 3.12 | ~ | Cytoplasm | other |
IFITM3 | interferon induced transmembrane protein 3 | 3.48 | ~ | Plasma membrane | other |
ISG15 | ISG15 ubiquitin-like modifier | 3.53 | ~ | Extracellular space | other |
NEDD9 | neural precursor cell expressed, developmentally down-regulated 9 | 2.59 | ~ | Nucleus | other |
S100A4 | S100 calcium binding protein A4 | 4.73 | ~ | Cytoplasm | other |
SERPINA3 | serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 | 58.49 | 2.51 | Extracellular space | other |
TNFAIP6 | tumor necrosis factor, alpha-induced protein 6 | 3.02 | ~ | Extracellular space | other |
Orphan | Â | Â | Â | Â |
MGLL | monoglyceride lipase | -7.85 | -18.15 | Plasma membrane | enzyme |
MYO9B | myosin IXB | 2.18 | ~ | Cytoplasm | enzyme |
PAFAH1B1 | platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45 kDa) | ~ | -2.86 | Cytoplasm | enzyme |
PDE4B | phosphodiesterase 4B, cAMP-specific | 5.60 | 2.36 | Cytoplasm | enzyme |
DEK | DEK oncogene | -3.01 | -7.35 | Nucleus | transcription regulator |
TCF12 | transcription factor 12 | 2.16 | ~ | Nucleus | transcription regulator |
IGSF6 | immunoglobulin superfamily, member 6 | 22.46 | 3.27 | Plasma membrane | transmembrane receptor |
THBD | thrombomodulin | 3.85 | 2.09 | Plasma membrane | transmembrane receptor |
TGFB2 | transforming growth factor, beta 2 | -4.00 | -7.97 | Extracellular space | growth factor |
KCNN4 | potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 | 3.09 | -9.43 | Plasma membrane | ion channel |
PRSS23 | protease, serine, 23 | 4.05 | ~ | Extracellular space | peptidase |
PTPN4 | protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) | 4.49 | 2.21 | Cytoplasm | phosphatase |
CALB1 | calbindin 1, 28 kDa | -2.09 | ~ | Cytoplasm | other |
CLEC12A | C-type lectin domain family 12, member A | 10.29 | 2.15 | Plasma membrane | other |
LCP1 | lymphocyte cytosolic protein 1 (L-plastin) | 6.08 | 2.80 | Cytoplasm | other |
LSP1 | lymphocyte-specific protein 1 | 11.72 | 2.14 | Cytoplasm | other |
MYO1F | myosin IF | 4.27 | 2.26 | Cytoplasm | other |
SERPING1 | serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 | 5.81 | 2.03 | Extracellular space | other |
Slpi (includes others) | secretory leukocyte peptidase inhibitor | 82.91 | 3.12 | unknown | other |