Table 1.

RNA-seq studies in human osteoarthritis.

Tissue	Comparison (sample size)	Gene ontology/Pathway	Reference
Cartilage	Normal (n = 18) vs. OA (n = 20)	Early growth response genes; transcription factors	[14]
	NOF (n = 6) vs. OA (n = 6)	Long intergenic non-coding RNAs	[15]
	Non-OA (n = 10) vs. OA (n = 44)	Mechanoreceptors; calcium signaling; ion channels; cytoskeletal organizers	[16]
	intact OA cartilage (n = 8) vs. damaged OA cartilage (n = 8)	Non-chondrogenic response of altered matrix protein and secreted proteinase expression	[17]
	APM (n = 10) vs. OA (n = 10)	Mesenchymal cell apoptosis; epithelial morphogenesis; canonical glycolysis; extracellular matrix organization; cartilage development; glucose catabolic process	[5]
Synovium	Low OA pain (n = 5) vs. High OA pain (n = 5)	Neuronal survival under cellular stress; calcium-dependent synaptic exocytosis; pain in synovial microenvironment	[18]
	Failed MoP (n = 6) vs. THA (n = 5)	Inflammation; redox homeostasis; metal ion binding and transport; macrophage activation; apoptosis	[19]
	Failed MoM (n = 16) vs. THA (n = 16)	Immune response; extracellular matrix	[20]
	Early RA, OA and others (multiple groups)	Leukocyte activation; T cell activation; B cell mediated immunity; osteoblast differentiation; bone remodeling; epidermal growth factor receptor signaling pathway	[21]
Meniscus	APM (n = 12) vs. OA (n = 12)	Response to external stimuli; cell migration and localization; histone deacetylase activity; skeletal development	[6]
Facet joint tissues	Moderate degeneration (n = 20) vs. severe degeneration (n = 28)	Wnt signaling; NFκ-B signaling	[22]

OA = osteoarthritis; NOF = neck of femur fracture; APM = arthroscopic partial meniscectomy; MoP = metal on plastic; THA = total hip arthroplasty; MoM = metal on metal; RA = rheumatoid arthritis; Wnt = Wingless and the name Int-1; NF-κB = nuclear factor kappa-light-chain-enhancer of activated B cells.