Table 4 Summary of biological processes and associated genes reported in the included studies
From: Genomic analyses of early peri-implant bone healing in humans: a systematic review
Process | Upregulated genes |
|---|---|
Category (gene code) | |
Inflammation/immune response | |
  Pro-inflammatory cytokines | Tumor necrosis factor (TNF-a, TNFSF9) |
Interleukin (IL-6, IL-2, IL-1Â F9, IL-23A, IL-6ST) | |
Interferon (IFNA2) | |
Nuclear factor-kB (I-kB kinase/NF-kB) | |
  Anti-inflammatory cytokines | Interleukin (IL-22, IL-9) |
Toll interacting protein (TOLLIP) | |
  Cells | Lymphocyte, macrophage negative proliferation (BTLA, LST1) |
Macrophage scavenger receptor (MSR1) | |
  Chemotaxis | Chemokines (CCR8, CCL18, CCL22, CXCL10, CXCL14) |
Osteoinduction/osteogenesis | |
Growth factors (GF)/signaling pathways | Insulin-like GF (IGF1) |
Transforming GF (TGF-b, TGF-b receptor 1, 2 and 3, TGF-a) | |
Platelet-derived GF (PDGF receptor) | |
Bone morphogenetic proteins (BMP4, BMP6, BMP receptor 1A, BMP2-K) | |
Growth and differentiation factor (GDF10) | |
Wnt frizzled receptor (FZD3, FZD8, FRZB) | |
Notch (NOTCH2) | |
Ras-protein signal transduction (RAP1B, RAP1A, RASGRP4) | |
Mitogen activated protein kinase (MAP3K7IP2, MAPK9, MAP2K3, MAP3K2) | |
  Transcription factors | ‘Master switches’ [RUNX2, SP7 (OSX)] |
Homeobox (DLX1, DLX5, HOXD12, MSX1, HOXA5, HOXB1, HOXB6, HOXC6) | |
SP [SP1, SP3, SP7 (Osx)] | |
Twist (TWIST 1-receptor) | |
  ECM deposition/organization | Collagen (Col1A1, Col12A1, Col6A3, Col3A1, Col6A1, Col11A1, Col11A2, Col13A1, Col5A2) |
Non-collagen proteins [BGLAP (OC), SPARC (ON), SPP1 (OP), BSP, IBSP, POSTN, ECM1] | |
| Â | Small leucine-rich proteoglycans (SLRP) (DCN, BGN, LUM) |
Heat-shock protein 47 (HSP47) | |
Alkaline phosphatase (ALPL) | |
Cadherin (CDH11) | |
Integrin (ITGB4, ITGB5) | |
Laminin (LAMA2, LAMA3) | |
Pro-collagen lysyl-hydroxylase (PLOD1, PLOD2, PLOD3) | |
Pro-collagen C-endopeptidase enhancer (PCOLCE) | |
Lysyl-oxidase (LOX) | |
Osteoclast activity/remodeling | Cathepsin K (CTSK, CTSK-receptor) |
Tartarate-resistant acid phosphatase (TRAP/ACP5) | |
Matrix metallopeptidase (MMP2, MMP12, MMP9, MMP7, MMP13) | |
Tissue inhibitor metallopeptidase (TIMP2, TIMP3) | |
Angiogenesis | Vascular endothelial GF-signaling (EPAS1, ANXA2, EGR1-binding protein) |
Phosphatidyl-inositol 3-kinase (PI3K)-Akt signaling | |
Neurogenesis | Brain-derived neurotrophic factor (BDNF) |
Neurotrophin 3 (NTF3) | |
NK2 homeobox 2(NKX2-2) | |
Tubby-like protein 3 (TULP3) | |