Supplementary table 3: The microarray data analysis results from the performed comparative analyses between controls, patients before and after infliximab treatment in UC, CDc, IBDc and CDi [fold change (FC), average log2 gene expression level across all arrays involved in the comparative analysis (AveExpr), p-value and FDR] for the filtered probe sets (probe sets with an intensity > log2(50) in at least 10% of the samples) representing MMP, TIMP, ADAM(TS) and growth factor genes. R: responders, NR: non-responders. The abbreviations of the tissue remodeling genes are explained in supplementary table 1. Probe Set ID Gene Symbol UC before therapy (n=24) CDi before therapy (n=18) vs vs CDc before therapy (n=19) CDc before therapy (n=19) FC AveExpr p-value FDR FC AveExpr p-value FDR MMP genes 204475_at MMP1 0.92 10.38 0.82 0.98 1.12 10.53 0.76 0.92 201069_at MMP2 1.01 8.08 0.98 1.00 0.80 7.92 0.46 0.75 205828_at MMP3 1.01 10.42 0.97 1.00 0.47 9.88 0.08 0.30 204259_at MMP7 1.97 8.32 0.02 0.46 0.44 7.20 0.01 0.06 203936_s_at MMP9 1.06 8.07 0.79 0.98 0.46 7.47 0.01 0.06 205680_at MMP10 1.76 6.94 0.09 0.71 0.52 6.03 0.10 0.36 204580_at MMP12 1.27 10.91 0.19 0.81 0.38 10.05 0.00 0.03 160020_at MMP14 1.17 6.41 0.05 0.60 0.97 6.26 0.60 0.83 202827_s_at MMP14 1.30 5.98 0.06 0.65 0.90 5.69 0.45 0.75 202828_s_at MMP14 1.17 6.45 0.08 0.69 0.98 6.31 0.86 0.95 203365_s_at MMP15 0.99 6.76 0.91 0.99 1.18 6.88 0.09 0.33 204574_s_at MMP19 1.01 5.52 0.89 0.99 1.03 5.54 0.58 0.82 204575_s_at MMP19 1.12 5.67 0.54 0.94 0.78 5.40 0.23 0.54 227106_at MMP19 1.02 5.54 0.67 0.96 1.08 5.58 0.11 0.36 221953_s_at MMP24 /// LOC729580 0.96 7.01 0.56 0.94 1.02 7.06 0.71 0.89 49679_s_at MMP24 /// LOC729580 0.98 6.81 0.63 0.96 1.02 6.85 0.70 0.89 207890_s_at MMP25 1.14 5.71 0.06 0.65 1.09 5.67 0.36 0.68 219909_at MMP28 0.99 5.05 0.97 1.00 0.90 4.99 0.41 0.72 222937_s_at MMP28 1.04 5.92 0.53 0.94 0.96 5.85 0.60 0.84 224207_x_at MMP28 1.02 6.79 0.69 0.96 1.04 6.80 0.61 0.84 239272_at MMP28 0.86 6.21 0.18 0.80 0.86 6.22 0.12 0.38 239273_s_at MMP28 0.94 6.31 0.55 0.94 0.88 6.27 0.18 0.48 TIMP genes 201666_at TIMP1 1.51 10.55 0.01 0.42 0.63 9.89 0.04 0.19 203167_at TIMP2 1.31 6.72 0.04 0.57 1.15 6.60 0.26 0.58 224560_at TIMP2 1.21 7.89 0.27 0.86 0.92 7.68 0.67 0.87 231579_s_at TIMP2 1.24 9.08 0.22 0.83 0.98 8.89 0.93 0.98 201147_s_at TIMP3 1.07 4.84 0.68 0.96 0.79 4.61 0.19 0.50 201148_s_at TIMP3 1.09 6.43 0.22 0.83 0.92 6.31 0.24 0.55 201149_s_at TIMP3 1.07 5.26 0.71 0.97 0.75 5.00 0.14 0.43 201150_s_at TIMP3 1.27 6.09 0.25 0.84 0.69 5.64 0.16 0.45 ADAM genes 205180_s_at ADAM8 1.09 5.77 0.47 0.93 1.06 5.75 0.66 0.87 1555326_a_at ADAM9 1.40 7.72 0.03 0.55 0.69 7.19 0.05 0.22 202381_at ADAM9 1.19 10.04 0.08 0.68 0.83 9.77 0.10 0.36 202604_x_at ADAM10 1.16 6.61 0.14 0.77 0.86 6.39 0.20 0.50 214895_s_at ADAM10 1.06 6.61 0.68 0.96 0.79 6.40 0.13 0.40 1555896_a_at ADAM15 1.06 6.91 0.34 0.89 0.81 6.72 0.00 0.04 217007_s_at ADAM15 1.07 5.86 0.41 0.91 0.80 5.65 0.03 0.16 205745_x_at ADAM17 0.98 6.19 0.69 0.96 0.89 6.12 0.11 0.36 209765_at ADAM19 1.11 6.19 0.41 0.91 0.81 5.96 0.16 0.45 205997_at ADAM28 1.32 6.03 0.14 0.77 1.46 6.07 0.08 0.31 208269_s_at ADAM28 1.11 5.35 0.06 0.63 1.04 5.30 0.47 0.76 233868_x_at ADAM33 1.00 6.76 0.97 1.00 1.09 6.82 0.40 0.71 206134_at ADAMDEC1 0.65 8.30 0.02 0.48 1.16 8.75 0.41 0.71 222162_s_at ADAMTS1 1.28 5.74 0.31 0.88 0.73 5.32 0.21 0.53 235368_at ADAMTS5 1.05 5.45 0.69 0.96 1.42 5.65 0.01 0.08 220705_s_at ADAMTS7 1.02 5.41 0.84 0.98 1.15 5.50 0.13 0.40 226814_at ADAMTS9 1.40 6.53 0.02 0.45 0.62 5.92 0.00 0.03 220208_at ADAMTS13 0.97 5.73 0.56 0.94 0.89 5.67 0.04 0.18 Growth factor genes 212285_s_at AGRN 1.19 6.85 0.03 0.52 0.85 6.59 0.06 0.25 217410_at AGRN 1.10 5.41 0.17 0.79 1.02 5.34 0.79 0.92 217419_x_at AGRN 1.14 6.61 0.10 0.73 0.82 6.36 0.03 0.16 202834_at AGT 1.33 5.90 0.05 0.60 1.00 5.66 0.98 0.99 213001_at ANGPTL2 1.07 6.60 0.75 0.97 0.73 6.33 0.17 0.47 213004_at ANGPTL2 1.02 5.04 0.88 0.99 0.78 4.85 0.12 0.38 221009_s_at ANGPTL4 1.50 6.16 0.00 0.20 1.29 6.01 0.06 0.26 223333_s_at ANGPTL4 1.32 5.37 0.02 0.49 1.21 5.29 0.15 0.43 205239_at AREG 1.42 8.63 0.04 0.60 0.23 7.31 0.00 0.00 210237_at ARTN 1.01 5.66 0.85 0.98 0.82 5.51 0.01 0.06 202701_at BMP1 0.95 6.07 0.42 0.91 0.91 6.04 0.08 0.31 205574_x_at BMP1 1.06 5.56 0.57 0.95 0.84 5.39 0.08 0.30 206725_x_at BMP1 1.08 5.36 0.23 0.83 1.03 5.32 0.71 0.89 207595_s_at BMP1 1.01 5.70 0.86 0.99 0.86 5.58 0.04 0.19 205289_at BMP2 1.11 8.88 0.31 0.88 0.42 8.19 0.00 0.00 205290_s_at BMP2 1.19 8.21 0.12 0.74 0.42 7.46 0.00 0.00 211518_s_at BMP4 1.11 5.52 0.17 0.80 0.98 5.42 0.75 0.91 211260_at BMP7 0.94 5.79 0.13 0.76 0.99 5.83 0.84 0.94 220203_at BMP8A 1.01 5.55 0.88 0.99 0.98 5.53 0.76 0.92 218529_at CD320 1.07 7.10 0.27 0.86 0.67 6.77 0.00 0.00 219505_at CECR1 1.19 7.29 0.32 0.88 0.66 6.86 0.03 0.15 219500_at CLCF1 1.15 5.59 0.03 0.52 0.90 5.40 0.07 0.29 207442_at CSF3 1.18 6.03 0.28 0.86 1.00 5.90 0.99 1.00 209101_at CTGF 1.32 7.64 0.11 0.73 0.42 6.82 0.00 0.00 205767_at EREG 1.75 6.65 0.04 0.56 0.40 5.56 0.01 0.06 218255_s_at FBRS 1.01 6.09 0.89 0.99 1.09 6.14 0.10 0.34 204421_s_at FGF2 1.11 5.18 0.36 0.90 0.79 4.93 0.04 0.19 208417_at FGF6 1.04 5.52 0.39 0.91 1.03 5.51 0.61 0.84 1554741_s_at FGF7 /// KGFLP1 /// 1.13 5.00 0.64 0.96 0.68 4.62 0.16 0.45 KGFLP2 206404_at FGF9 0.70 4.60 0.00 0.26 2.57 5.55 0.00 0.00 221136_at GDF2 1.05 5.85 0.38 0.90 1.05 5.85 0.35 0.67 206614_at GDF5 0.99 5.80 0.89 0.99 1.02 5.82 0.71 0.89 221577_x_at GDF15/// LOC100287132 1.18 6.52 0.20 0.82 0.61 6.03 0.00 0.02 /// LOC100292463 202543_s_at GMFB 0.98 8.31 0.81 0.98 0.74 8.11 0.00 0.04 202544_at GMFB 0.90 8.77 0.02 0.49 0.94 8.81 0.29 0.61 204220_at GMFG 1.18 7.09 0.30 0.87 0.88 6.87 0.49 0.77 208308_s_at GPI 1.07 9.76 0.22 0.83 0.83 9.58 0.01 0.06 200678_x_at GRN 0.93 9.16 0.32 0.88 0.79 9.05 0.00 0.03 211284_s_at GRN 0.97 8.47 0.62 0.95 0.83 8.37 0.01 0.10 216041_x_at GRN 0.95 9.13 0.47 0.93 0.79 9.00 0.00 0.03 203821_at HBEGF 1.56 7.57 0.04 0.57 0.51 6.74 0.01 0.05 38037_at HBEGF 1.49 7.31 0.05 0.62 0.61 6.64 0.02 0.11 200896_x_at HDGF 1.10 9.32 0.02 0.47 1.23 9.39 0.00 0.01 216484_x_at HDGF 1.04 8.56 0.24 0.84 1.17 8.63 0.01 0.05 209524_at HDGFRP3 1.03 5.73 0.89 0.99 0.59 5.34 0.02 0.11 209526_s_at HDGFRP3 0.97 5.45 0.81 0.98 0.64 5.17 0.01 0.07 216693_x_at HDGFRP3 0.94 5.60 0.67 0.96 0.61 5.30 0.01 0.05 211577_s_at IGF1 1.02 5.60 0.73 0.97 0.99 5.57 0.80 0.93 202409_at IGF2 /// INS-IGF2 1.06 5.11 0.69 0.97 1.07 5.12 0.66 0.87 210511_s_at INHBA 1.19 5.72 0.56 0.94 0.92 5.52 0.81 0.93 209098_s_at JAG1 1.21 6.66 0.15 0.78 0.53 6.06 0.00 0.01 209099_x_at JAG1 1.10 10.29 0.14 0.77 0.64 9.89 0.00 0.00 216268_s_at JAG1 1.10 10.30 0.18 0.80 0.60 9.87 0.00 0.00 231183_s_at JAG1 0.98 6.00 0.89 0.99 0.56 5.62 0.00 0.02 209784_s_at JAG2 1.13 5.33 0.06 0.64 1.30 5.41 0.00 0.02 32137_at JAG2 1.08 5.75 0.28 0.86 1.34 5.89 0.00 0.02 226534_at KITLG 0.69 7.83 0.00 0.16 0.71 7.89 0.00 0.04 206268_at LEFTY1 0.68 8.99 0.03 0.52 0.06 7.33 0.00 0.00 205266_at LIF 1.36 5.99 0.00 0.19 0.87 5.64 0.07 0.29 1559361_at MACC1 1.15 4.29 0.12 0.75 2.17 4.72 0.00 0.00 1566764_at MACC1 1.27 3.85 0.09 0.70 3.31 4.49 0.00 0.00 1566766_a_at MACC1 1.22 5.24 0.00 0.22 2.30 5.67 0.00 0.00 232151_at MACC1 1.15 4.98 0.12 0.75 2.50 5.51 0.00 0.00 202655_at MANF 1.14 9.29 0.02 0.45 0.74 8.97 0.00 0.00 209035_at MDK 0.89 8.01 0.36 0.90 1.37 8.33 0.02 0.13 206560_s_at MIA 1.12 6.12 0.43 0.92 0.90 5.95 0.40 0.71 205614_x_at MST1 1.02 6.25 0.75 0.97 2.41 6.85 0.00 0.00 216320_x_at MST1 1.04 6.27 0.61 0.95 2.69 6.94 0.00 0.00 214075_at NENF 0.97 5.92 0.63 0.96 0.89 5.85 0.02 0.13 218407_x_at NENF 0.98 7.89 0.57 0.95 0.92 7.85 0.10 0.34 208232_x_at NRG1 1.09 5.17 0.15 0.78 1.00 5.10 0.99 1.00 230329_s_at NUDT6 0.77 6.13 0.00 0.26 0.64 6.02 0.00 0.00 219475_at OSGIN1 1.07 5.34 0.32 0.88 1.48 5.56 0.00 0.00 214637_at OSM 1.15 5.21 0.25 0.84 1.11 5.17 0.50 0.78 230170_at OSM 1.50 5.08 0.10 0.71 1.21 4.89 0.50 0.78 205463_s_at PDGFA 0.99 7.02 0.88 0.99 1.11 7.10 0.12 0.39 216867_s_at PDGFA 1.02 5.15 0.79 0.98 1.15 5.23 0.14 0.42 229830_at PDGFA 0.89 7.80 0.22 0.83 1.13 7.98 0.18 0.48 216061_x_at PDGFB 1.10 5.51 0.04 0.60 1.00 5.43 0.93 0.98 218718_at PDGFC 1.00 5.35 0.99 1.00 2.03 5.85 0.00 0.00 225064_at RABEP1 1.04 6.42 0.54 0.94 1.00 6.39 1.00 1.00 225092_at RABEP1 1.12 6.79 0.17 0.79 1.11 6.78 0.28 0.60 219057_at RABEP2 1.02 5.50 0.67 0.96 1.14 5.58 0.03 0.16 74694_s_at RABEP2 0.89 6.38 0.10 0.73 1.07 6.51 0.33 0.65 77508_r_at RABEP2 1.00 6.42 0.98 1.00 1.03 6.44 0.59 0.83 209752_at REG1A 0.65 11.45 0.31 0.88 2.84 12.53 0.01 0.07 206286_s_at TDGF1 /// TDGF3 0.93 5.89 0.62 0.95 0.51 5.47 0.00 0.00 205009_at TFF1 1.59 12.12 0.00 0.20 1.25 11.90 0.23 0.54 214476_at TFF2 1.48 7.45 0.08 0.68 1.86 7.57 0.11 0.36 204623_at TFF3 0.88 11.37 0.22 0.83 1.12 11.56 0.21 0.52 205016_at TGFA 0.94 7.34 0.59 0.95 1.07 7.43 0.52 0.79 211258_s_at TGFA 0.98 5.39 0.73 0.97 0.98 5.39 0.61 0.84 203085_s_at TGFB1 1.20 5.69 0.38 0.90 0.99 5.54 0.95 0.99 204858_s_at TYMP 1.14 7.27 0.20 0.82 1.10 7.24 0.39 0.70 210512_s_at VEGFA 1.25 9.23 0.01 0.35 1.21 9.18 0.02 0.14 210513_s_at VEGFA 1.31 6.52 0.01 0.31 1.15 6.40 0.15 0.43 211527_x_at VEGFA 1.39 6.16 0.00 0.19 1.11 5.97 0.29 0.61 212171_x_at VEGFA 1.26 7.22 0.00 0.15 1.12 7.11 0.08 0.30 209946_at VEGFC 1.04 4.89 0.77 0.98 1.01 4.86 0.96 0.99 205586_x_at VGF 1.11 5.29 0.06 0.64 1.06 5.25 0.25 0.57 Probe Set ID Gene Symbol UC before therapy CDc before therapy IBDc before therapy CDi before therapy (n=24) (n=19) (n=43) (n=18) vs vs vs vs control colons control colons control colons control ileums (n=6) (n=6) (n=6) (n=6)