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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-1 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)
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]
  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)