Table 3.

Probe set IDs of the Affymetrix mouse genome 430 2.0 array, official gene symbols and titles, and relative fold changes with respective P‐values for probe sets related to extracellular matrix molecules, glycosaminoglycan degradation and matrix metalloproteinases/tissue inhibitors of metalloproteinases (MMPs/TIMPs), and differentially expressed between TMEV‐infected and mock‐infected mice in the time course of TME. Abbreviations: dpi = days post‐infection; aka = also known as; MMP = matrix metalloproteinase; TIMP = tissue inhibitors of metalloproteinase; TMEV = Theiler's murine encephalomyelitis virus; TME = Theiler's murine encephalomyelitis.

Gene symbol	Probe set ID	Gene title	14 dpi		42 dpi		98 dpi		196 dpi
			Fold change	P‐value	Fold change	P‐value	Fold change	P‐value	Fold change	P‐value
Extracellular matrix molecules
Agc1	1449827_at	Aggrecan 1	−1.09*	0.041	−1.13*	0.041	−1.21*	0.004	−1.16	0.065
Bgn	1437889_x_at	Biglycan	1.19	0.394	1.14	0.093	1.07	0.537	1.56*	0.002
Bgn	1416405_at	Biglycan	1.22	0.394	1.31*	0.015	1.21	0.126	1.88*	0.002
Bgn	1448323_a_at	Biglycan	1.26	0.180	1.28*	0.015	1.19	0.177	1.84*	0.002
Col1a1	1423669_at	Procollagen type I alpha 1	2.05	0.240	1.07	0.180	−1.18	0.662	1.50*	0.004
Col1a2	1450857_a_at	Procollagen type I alpha 2	1.58	0.180	1.20	0.240	−1.15	0.537	1.75*	0.002
Col1a2	1423110_at	Procollagen type I alpha 2	1.51	0.394	−1.10	0.937	−1.28	0.429	1.60*	0.004
Col3a1	1427883_a_at	Procollagen type III alpha 1	1.28	0.485	1.29	0.093	1.03	0.931	2.35*	0.009
Col4a1	1452035_at	Procollagen type IV alpha 1	1.09*	0.041	1.11	0.180	−1.03	0.662	1.19	0.132
Col5a1	1416740_at	Procollagen type V alpha 1	1.33	0.240	1.10	0.240	1.03	0.429	1.34*	0.004
Col5a1	1434479_at	Procollagen type V alpha 1	1.10	0.485	−1.11	0.180	−1.12*	0.017	1.05	0.485
Col5a2	1422437_at	Procollagen type V alpha 2	1.21	0.394	1.10	0.394	−1.04	0.662	1.41*	0.026
Col6a1	1448590_at	Procollagen type VI alpha 1	1.31	0.394	1.11	0.394	−1.07	0.429	1.62*	0.002
Col6a2	1452250_a_at	Procollagen type VI alpha 2	1.23	0.132	1.03	0.589	−1.14	0.247	1.38*	0.015
Col6a2	1426947_x_at	Procollagen type VI alpha 2	1.11	0.240	1.13	0.180	−1.10	0.329	1.19*	0.015
Col6a3 /// LOC674521	1424131_at	Procollagen type VI alpha 3 /// similar to alpha 3 type VI collagen isoform 1 precursor	1.25	0.394	1.13	0.589	1.25*	0.009	1.36*	0.015
Col8a1	1418440_at	Procollagen type VIII alpha 1	1.07	0.240	−1.06	0.589	1.07	0.662	1.23*	0.041
Col8a2	1434667_at	Procollagen type VIII alpha 2	−1.00	0.937	−1.05	0.937	−1.14	0.126	1.35*	0.009
Col9a3	1460734_at	Procollagen type IX alpha 3	1.07	0.180	−1.10	0.310	1.23*	0.004	1.06	0.394
Col13a1	1422866_at	Procollagen type XIII alpha 1	1.05	0.818	1.08	0.485	−1.14*	0.004	1.09	0.310
Col14a1	1427168_a_at	Procollagen type XIV alpha 1	−1.05	0.937	−1.15	0.699	−1.26	0.247	1.48*	0.041
Col15a1	1448755_at	Procollagen type XV	−1.01	0.937	1.11	0.394	−1.11*	0.030	1.14	0.132
Col16a1	1427986_a_at	Procollagen type XVI alpha 1	1.29*	0.009	1.41*	0.004	1.45*	0.004	1.44*	0.009
Col18a1	1426955_at	Procollagen type XVIII alpha 1	1.13	0.065	1.06	0.310	1.04	0.537	1.29*	0.015
Col19a1	1421698_a_at	Procollagen type XIX alpha 1	1.21	0.132	−1.14	0.394	−1.21	0.537	−1.30*	0.009
Col20a1	1425234_at	Collagen type XX alpha 1	1.16*	0.026	1.22*	0.015	1.65*	0.004	1.44*	0.015
Col20a1	1430855_at	Collagen type XX alpha 1	1.05	0.394	1.31*	0.009	1.28	0.052	1.02	0.589
Col22a1	1453084_s_at	Collagen type XXII alpha 1	1.10	0.818	1.05	0.699	−1.15*	0.030	1.01	0.589
Col27a1	1429549_at	Procollagen type XXVII alpha 1	1.22*	0.026	1.16	0.699	−1.03	0.792	1.10	0.180
Cspg2	1427256_at	Chondroitin sulfate proteoglycan 2 (aka neurocan)	1.04	0.818	1.08	0.240	1.49*	0.004	1.40*	0.026
Cspg2	1427257_at	Chondroitin sulfate proteoglycan 2 (aka neurocan)	−1.21*	0.041	1.06	0.699	1.26*	0.004	1.02	0.699
Cspg3	1423604_at	Chondroitin sulfate proteoglycan 3 (aka neurocan)	1.01	0.818	1.16*	0.009	1.11*	0.030	−1.02	0.485
Cspg3	1434679_at	Chondroitin sulfate proteoglycan 3 (aka neurocan)	1.11*	0.002	1.37*	0.002	1.59*	0.004	1.48*	0.002
Dcn	1449368_at	Decorin	1.29	0.394	1.25	0.310	−1.34	0.247	1.94*	0.002
Eln	1420854_at	Elastin	−1.03	0.589	−1.04	0.394	−1.06	0.429	−1.19*	0.009
Fn1	1426642_at	Fibronectin 1	1.37	0.180	1.48*	0.009	1.32*	0.030	1.61*	0.004
Hapln1	1438020_at	Hyaluronan and proteoglycan link protein 1	−1.34*	0.015	−1.19*	0.009	−1.19	0.177	−1.26*	0.009
Lama2	1426285_at	Laminin alpha 2	−1.06	0.699	−1.04	0.937	−1.20*	0.009	1.14	0.180
Lama3	1444860_at	Laminin alpha 3	−1.04	0.485	−1.03	0.818	1.04	0.329	−1.17*	0.026
Lama3 /// LOC669814	1427512_a_at	Laminin alpha 3 /// similar to Laminin alpha‐3 chain precursor (Nicein alpha subunit)	1.01	0.937	−1.01	0.937	1.01	1.000	1.40*	0.026
Lama4	1424807_at	Laminin alpha 4	1.01	0.699	1.03	0.699	1.02	0.429	1.41*	0.004
Lama5 /// LOC671909	1427009_at	Laminin alpha 5 /// similar to Laminin alpha‐5 chain precursor	−1.06	0.240	1.02	0.589	−1.12	0.177	1.12*	0.026
Lamb1‐1	1424114_s_at	Laminin B1 subunit 1	1.01	0.937	−1.05	0.589	−1.14	0.082	1.34*	0.026
Lamb2	1416513_at	Laminin beta 2	1.03	0.699	−1.01	0.485	−1.08	0.537	1.32*	0.004
Lamc1	1423885_at	Laminin gamma 1	1.11	0.065	1.04	0.818	1.12	0.126	1.26*	0.009
Lamc2	1421279_at	Laminin gamma 2	1.09	0.240	1.17*	0.026	1.07	0.247	1.01	0.937
Nid2	1423516_a_at	Nidogen 2 (aka entactin)	1.02	0.310	1.30*	0.041	1.21	0.052	1.49*	0.026
Ptprz1	1452284_at	Protein tyrosine phosphatase, receptor type Z, polypeptide 1 (aka phosphacan)	−1.04	0.310	−1.12*	0.015	−1.08	0.052	−1.11*	0.026
Tnc	1416342_at	Tenascin C	1.33	0.093	1.38*	0.004	1.33*	0.017	1.26	0.394
Enzymes of glycosaminoglycan degradation
Arsb	1429190_at	Arylsulfatase B	−1.05	0.310	1.18*	0.041	1.24	0.537	1.41	0.093
Galns	1448744_at	Galactosamine (N‐acetyl)‐6‐sulfate sulfatase	−1.04	0.818	1.34*	0.002	1.50*	0.004	1.58*	0.002
Gns	1433488_x_at	Glucosamine (N‐acetyl)‐6‐sulfatase	1.18*	0.009	1.62*	0.002	2.09*	0.004	1.81*	0.002
Gns	1433546_at	Glucosamine (N‐acetyl)‐6‐sulfatase	1.19*	0.002	1.57*	0.002	1.89*	0.004	1.81*	0.002
Gns	1446861_at	Glucosamine (N‐acetyl)‐6‐sulfatase	1.28*	0.015	−1.00	0.937	1.24	0.082	1.05	0.699
Gusb	1430332_a_at	Glucuronidase, beta	−1.26	0.132	1.05	0.699	1.13	0.662	1.45*	0.009
Gusb	1448124_at	Glucuronidase, beta	1.19*	0.041	2.15*	0.002	3.10*	0.004	3.30*	0.002
Hexa	1449024_a_at	Hexosaminidase A	1.13	0.065	1.53*	0.002	1.98*	0.004	2.04*	0.002
Hexb	1437874_s_at	Hexosaminidase B	1.18	0.093	1.64*	0.002	1.96*	0.004	1.75*	0.002
Hexb	1460180_at	Hexosaminidase B	1.34*	0.004	1.96*	0.002	2.39*	0.004	2.24*	0.002
Hpse	1433930_at	Heparanase	1.08	0.394	2.80*	0.002	8.53*	0.004	10.22*	0.002
Hyal1 /// Nat6	1449954_at	Hyaluronoglucosaminidase 1 /// N‐acetyltransferase 6	−1.03	0.589	−1.03	0.589	1.02	0.792	1.26*	0.002
Ids	1427813_at	Iduronate 2‐sulfatase	−1.03	0.485	−1.11*	0.041	1.01	0.792	1.01	0.937
Ids	1455481_at	Iduronate 2‐sulfatase	−1.01	0.818	−1.08*	0.026	−1.15*	0.017	−1.10*	0.002
Idua	1418793_at	Iduronidase alpha‐L‐	1.03	0.394	1.11*	0.026	1.19	0.052	1.06	0.132
Idua	1439251_at	Iduronidase alpha‐L‐	1.00	0.818	1.23*	0.002	1.16	0.052	1.07	0.310
Naglu	1417706_at	Alpha‐N‐acetylglucosaminidase (Sanfilippo disease IIIB)	1.05	0.818	1.91*	0.002	2.92*	0.004	3.18*	0.002
Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs)
Mmp2	1416136_at	Matrix metallopeptidase 2	−1.03	0.937	1.00	0.818	1.08	0.429	1.61*	0.002
Mmp2	1439364_a_at	Matrix metallopeptidase 2	1.04	0.937	1.13	0.240	1.13	0.429	1.64*	0.002
Mmp3	1418945_at	Matrix metallopeptidase 3	1.07	0.394	1.02	0.818	1.22*	0.017	1.28	0.310
Mmp9	1448291_at	Matrix metallopeptidase 9	−1.15	0.310	−1.28*	0.004	−1.14	0.177	−1.02	0.937
Mmp9	1416298_at	Matrix metallopeptidase 9	−1.06	0.589	−1.12*	0.041	−1.11	0.429	−1.08	0.310
Mmp12	1449153_at	Matrix metallopeptidase 12	1.02	0.589	1.47*	0.026	5.26*	0.004	6.89*	0.002
Mmp13	1417256_at	Matrix metallopeptidase 13	1.33	0.589	1.02	0.240	1.11	0.792	1.21*	0.015
Mmp14	1448383_at	Matrix metallopeptidase 14 (membrane‐inserted)	1.09	0.485	1.37*	0.041	1.08	0.537	1.41	0.240
Mmp14	1440920_at	Matrix metallopeptidase 14 (membrane‐inserted)	1.07	0.310	1.22*	0.026	−1.00	1.000	1.16	0.132
Mmp16	1440161_at	Matrix metallopeptidase 16	−1.05	0.394	1.13*	0.026	−1.16	0.537	−1.09	0.132
Mmp17	1448598_at	Matrix metallopeptidase 17	−1.02	0.589	−1.18*	0.004	−1.11	0.052	−1.17*	0.041
Mmp19	1421977_at	Matrix metallopeptidase 19	−1.02	0.937	1.01	0.937	1.47*	0.004	1.49*	0.002
Mmp23	1417281_a_at	Matrix metallopeptidase 23	1.09	0.394	1.03	0.240	−1.19*	0.030	1.16*	0.041
Mmp24	1417678_at	Matrix metallopeptidase 24	−1.10	0.240	−1.12*	0.041	−1.07	0.429	−1.05	0.699
Mmp24	1441456_at	Matrix metallopeptidase 24	−1.09	0.240	−1.15*	0.009	−1.07	0.329	−1.08*	0.041
Mmp24	1456376_at	Matrix metallopeptidase 24	−1.06*	0.041	−1.08	0.093	−1.18*	0.004	−1.09*	0.041
Mmp28	1447544_at	Matrix metallopeptidase 28 (epilysin)	−1.08	0.310	−1.04	0.589	−1.18*	0.017	1.08	0.310
Timp1	1460227_at	Tissue inhibitor of metalloproteinase 1	1.24	0.240	3.18*	0.002	4.56*	0.004	4.00*	0.002
Timp2	1460287_at	Tissue inhibitor of metalloproteinase 2	1.06	0.240	1.93*	0.002	2.67*	0.004	2.65*	0.002
Timp4	1450974_at	Tissue inhibitor of metalloproteinase 4	−1.15	0.310	−1.24*	0.015	−1.25*	0.017	−1.16	0.065
Timp4	1423405_at	Tissue inhibitor of metalloproteinase 4	−1.11	0.485	−1.20	0.093	−1.19*	0.017	−1.22*	0.026

^* Significant difference between TMEV‐infected and mock‐infected mice with P < 0.05 as detected by the Mann–Whitney U‐test.