Table 4.
Summary of biological processes and associated genes reported in the included studies
| 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) |
| 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] | |
| 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) | |