Table 4:

Significant associations between differences in gene expression levels and differences in phenotypes between DMM and SHAM knees.

Trait	Positive association with disease	Negative association with disease
Maximum OARSI score	Copz2, Csmd1, Col1a1, Wnt16, Casp3, Ank, Postn, Uaca	Rrp15, G0s2, Skap1
Summed OARSI score	Copz2, Csmd1, Kif26b, Col1a1, Wnt16, Tgfb2, Sgce, Bcl3, Scfd2, Lnx1, Ank, Cdk5rap3, Gpatch2, Postn, Myo1e, Uaca	Rrp15, G0s2, Skap1, Stab2
Synovitis score	Copz2, Csmd1, Kif26b, Col1a1, Timp3, Wnt16, Igf1, Trpm3, Nfe2l1, Tgfb2, Comp, Sgce, Bcl3, Scfd2, Gmds, Lnx1, Ank, Cdk5rap3, Gpatch2, Il1rl2, Postn, Myo1e, Aff3, Tmem2, Uaca	G0s2, Pcna
BV/TV	Copz2, Rasl11b, Col1a1, Timp3, Acan, Wnt16, Igf1, Mrpl10, Nfe2l1, Tgfb2, Comp, Sgce, Cdk5rap3, Gpatch2, Postn, Myo1e, Aff3	Pcna, Ulk1, Xrcc2
CDI	Copz2, Rasl11b, Col1a1, Tgfb2, Myo1e, Aff3	Pon2, Pcna, Ulk1
SMI	Copz2, Rasl11b, Col2a1, Col1a1, Timp3, Acan, Igf1, Tgfb2, Comp, Sgce, Cdk5rap3, Postn, Myo1e, Aff3	Tbx21, Pcna, Xrcc2
Tb.N	Rasl11b, Mrpl10	Xrcc2
Tb.T	Copz2, Rasl11b, Col1a1, Timp3, Wnt16, Igf1, Mrpl10, Nfe2l1, Tgfb2, Sgce, Fip1l1, Cdk5rap3, Gpatch2, Postn, Myo1e, Uaca	Tbx21, Ulk1, Xrcc2
Tb.Sp	Rasl11b, Myo1e, Aff3	Xrcc2
Subchondral bone plate thickness	None	None
# of ectopic calcifications	Col2a1, Col1a1, Timp3, Acan, Wnt16, Comp, Ank	Stab2

For trabecular architecture traits BV/TV, CDI, Tb.N, and Tb.Th, positive associations with disease are numerically negative associations as DMM is expected to reduce bone in trabeculae under the DMM operated knee. OARSI = Osteoarthritis Research Society International; BV/TV = bone volume fraction; CDI = connectivity density index; SMI = structure model index; Tb.N = trabecular number; Tb.Th = trabecular thickness; Tb.Sp = trabecular separation.