Table 3. Functional clustering of differentially expressed genes of hMSC-OP, hMSC-old and hMSC-senescent when compared to hMSC-C.

Symbol	Gene name		hMSC-OP	hMSC-old		hMSC-senescent			Reference
(1) Osteoblastogenesis
positive
PTH1R	parathyroid hormone 1 receptor		↑						[74]
IBSP	integrin-binding sialoprotein		↑						[75]
INHA	inhibin, alpha		↑						[76]
IGFBP2	insulin-like growth factor binding protein 2		↑						[77]
IGF2	insulin-like growth factor 2		↑			↓			[77]
VEGFB	vascular endothelial growth factor B		↑	↓					[78]
VEGFA	vascular endothelial growth factor A		↑	↓		↓			[78]
FOXC2	forkhead box C2 (MFH-1, mesenchyme forkhead 1)		↑	↓					[79]
COL1A1	collagen, type I, alpha 1			↓					[75]
RUNX2	runt-related transcription factor 2			↓					[75]
ANKH*	ankylosis, progressive homolog		↓	↓					[80]
SMAD3B	SMAD family member 3			↓					[81]
SPP1	secreted phosphoprotein 1					↓			[75]
EFNB2	ephrin-B2					↓			[82]
ALPL	alkaline phosphatase, liver/bone/kidney					↓			[80]
CYP2R1	cytochrome P450, family 2, subfamily R, polypeptide 1					↓			[80], [83]
FOXC1	forkhead box C1			↑		↓			[84]
IL6ST	interleukin 6 signal transducer (Oncostatin M receptor)			↓		↑			[85]
PDGFA	platelet-derived growth factor alpha polypeptide			↑					[11]
VDR	vitamin D receptor			↑					[80]
FGFR2*	fibroblast growth factor receptor 2			↑		↓			[86]
BMP6B	bone morphogenetic protein 6					↑			[11]
ROR1W	receptor tyrosine kinase-like orphan receptor 1		↓			↑			[87]
ANKRD6W	ankyrin repeat domain 6					↑			[16], [18]
negative
TGFB1	transforming growth factor, beta 1		↑	↓					[88]
MAB21L2B	mab-21-like 2		↑	↑					[15]
FST	follistatin		↑	↑					[89], [90]
FSTL3	follistatin-like 3		↑						[91]
KREMEN1W	kringle containing transmembrane protein 1		↑						[38]
SOSTW B	sclerostin		↑						[23]
FGFR1	fibroblast growth factor receptor 1		↑						[92]
IGFBP5	insulin-like growth factor binding protein 5		↑			↑			[11]
IGFBP4	insulin-like growth factor binding protein 4			↓					[11]
EGFR	epidermal growth factor receptor			↓					[93]
GREM2B	gremlin 2, cysteine knot superfamily, homolog		↓	↓					[94]
NOGB	noggin			↑					[11]
CTNNB1W	catenin, beta 1			↑					[17], [18]
SFRP4W	secreted frizzled-related protein 4					↑			[95]
WNT2W	wingless-type MMTV integration site family, member 2					↑			[17], [18]
WNT3W	wingless-type MMTV integration site family, member 3					↑			[17], [18]
(2) Osteoclastogenesis
positive
PTH1R	parathyroid hormone 1 receptor		↑						[25]
CSF1	colony stimulating factor 1		↑						[4]
PTGS2	prostaglandin-endoperoxide synthase 2		↑			↓			[96]
IGF2	insulin-like growth factor 2		↑			↓			[97]
TNFSF11	tumor necrosis factor superfamily, member 11					↓			[98]
SPP1	secreted phosphoprotein 1					↓			[99]
IL7	interleukin 7					↓			[100]
THBS1	thrombospondin 1					↑			[101]
IL1A*	interleukin 1, alpha			↓		↑			[67]
TNFSF10	tumor necrosis factor superfamily, member 10			↓		↓			[102]
TGFB2	transforming growth factor, beta 2			↓		↓			[103]
VEGFA	vascular endothelial growth factor A		↑	↓		↓			[46]
VEGFB	vascular endothelial growth factor B		↑	↓					[46]
TGFB1	transforming growth factor, beta 1		↑	↓					[47]
RUNX2	runt-related transcription factor 2			↓					[104]
negative
TNFRSF11B	tumor necrosis factor receptor superfamily, member 11b						↑		[98]
FSTL3	follistatin-like 3		↑						[105]
(3) Proliferation
positive
HMMR		hyaluronan-mediated motility receptor	↓					↓		[49]
HELLS		helicase, lymphoid-specific						↓		[106]
PTN		pleiotrophin						↓		[107]
SOD2		superoxide dismutase 2, mitochondrial			↓			↑		[108]
CCNB2		cyclin B2						↓		[109]
CDC2		cell division cycle 2, G1 to S and G2 to M	↓					↓		[109]
CCNA2		cyclin A2	↓		↓			↓		[109]
CCNE2		cyclin E2	↓		↓			↓		[109]
CCNF		cyclin F						↓		[110]
CCND1		cyclin D1						↑		[109]
CCND2		cyclin D2						↑		[109]
CDC25A		cell division cycle 25 homolog A						↓		[111]
CDC25B		cell division cycle 25 homolog B						↓		[112]
CDC25C		cell division cycle 25 homolog C						↓		[113]
CDK2		cyclin-dependent kinase 2			↓					[109]
negative
PSG1		pregnancy specific beta-1-glycoprotein 1						↑		[114]
PSG2		pregnancy specific beta-1-glycoprotein 2						↑		[114]
PSG3		pregnancy specific beta-1-glycoprotein 3			↓			↑		[114]
PSG4		pregnancy specific beta-1-glycoprotein 4						↑		[114]
PSG6		pregnancy specific beta-1-glycoprotein 6						↑		[114]
PSG7		pregnancy specific beta-1-glycoprotein 7						↑		[114]
ARHGAP29		Rho GTPase activating protein 29	↓					↑		[107]
CDKN2A		cyclin-dependent kinase inhibitor 2A						↑		[107]
CDKN1A		cyclin-dependent kinase inhibitor 1A	↑							[50]
(4) DNA-repair
positive
POLD1		polymerase (DNA directed), delta 1, catalytic subunit 125kDa						↓		[115]
POLE2		polymerase (DNA directed), epsilon 2 (p59 subunit)	↓					↓		[115]
POLQ		polymerase (DNA directed), theta						↓		[115]
POLH		polymerase (DNA directed), eta			↓					[115]
POLK		polymerase (DNA directed) kappa			↓					[115]
MRE11A		MRE11 meiotic recombination 11 homolog A			↓					[116]
PARP3		poly (ADP-ribose) polymerase family, member 3			↓					[117]
RAD50		RAD50 homolog	↓							[116]
RAD51		RAD51 homolog						↓		[116]
RAD51AP1		RAD51 associated protein 1	↓					↓		[118]
TOP2A		topoisomerase (DNA) II alpha 170 kDa	↓					↓		[119]
EXO1		exonuclease 1						↓		[116]
CHEK1		CHK1 checkpoint homolog						↓		[120]
HMGB2		high-mobility group box 2						↓		[121]

arrows pointing downward = at least 2fold reduced expression in comparison to hMSC-C; arrows pointing upward = at least 2fold enhanced expression in comparison to hMSC-C;

^W = gene associated with WNT signaling;

^B = gene associated with BMP signaling;

^* = probesets that refer to the gene are not identical in the indicated comparisons.