Table 2.

Differential gene expression for shear compared to axial specimens at each time point. Fold changes are shown on the left, and the corresponding q-values are shown on the right. Significant q-values (q < 0.2) and the associated fold changes are in bold.

Comparing treatments within time point
Genes grouped by functional type	Fold changes				q-values (FDR)
	Shear versus axial				Shear versus axial
	Day 0	Day 3	Day 7	Day 14	Day 0	Day 3	Day 7	Day 14
Cartilage matrix
Col1a1	5.29	4.93	0.54	0.14	0.09	0.09	0.43	0.05
Col2a1	0.55	2.46	0.41	1.07	0.27	0.12	0.12	0.88
Acan	0.66	1.15	1.21	2.07	0.43	0.68	0.68	0.13
Sox9	0.89	1.26	1.02	2.95	0.95	0.95	0.95	0.01
Opn	0.97	1.36	1.27	2.63	0.95	0.83	0.83	0.20
Comp	0.41	0.94	0.75	1.44	0.03	0.84	0.51	0.51
Degradative enzymes & inhibitors
Mmp1	2.84	1.13	0.49	0.37	0.32	0.84	0.32	0.32
Mmp3	2.36	1.62	3.19	0.56	0.45	0.50	0.41	0.50
Mmp13	0.34	5.51	0.26	0.71	0.14	0.05	0.08	0.60
Timp1	1.33	0.88	0.80	1.23	0.69	0.69	0.69	0.69
Timp2	2.63	2.36	0.71	1.58	0.06	0.06	0.39	0.33
Adamts5	2.02	1.49	0.82	0.14	0.52	0.66	0.74	0.01
Inflammatory response & signaling
Ihh	2.00	2.73	2.25	1.68	0.30	0.30	0.30	0.36
Tgfb	0.51	0.63	0.89	1.72	0.11	0.18	0.72	0.15
Inos	0.35	1.67	0.62	2.06	0.21	0.38	0.38	0.36
Chi3l1	1.08	0.54	1.05	1.61	0.92	0.57	0.92	0.57
Cell proliferation & apoptosis
Casp8	0.89	1.15	1.04	2.95	0.91	0.91	0.91	0.01
Fas	0.43	0.92	1.90	1.81	0.19	0.85	0.22	0.22