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) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 82.53 9.05 0.00 0.00 89.57 8.89 0.00 0.00 85.57 9.59 0.00 0.00 22.04 9.50 0.00 0.00 genes 201069_at MMP2 4.11 7.68 0.00 0.01 4.08 7.59 0.00 0.01 4.09 7.84 0.00 0.01 2.89 7.37 0.01 0.07 205828_at MMP3 68.33 9.21 0.00 0.00 67.44 8.96 0.00 0.00 67.93 9.68 0.00 0.00 47.58 7.93 0.00 0.00 204259_at MMP7 10.80 8.07 0.00 0.00 5.47 7.19 0.00 0.01 8.00 7.95 0.00 0.00 3.27 6.17 0.00 0.01 203936_s_at MMP9 8.02 7.51 0.00 0.00 7.56 7.32 0.00 0.00 7.81 7.71 0.00 0.00 1.63 6.71 0.30 0.61 205680_at MMP10 21.78 6.41 0.00 0.00 12.40 5.62 0.00 0.00 16.98 6.44 0.00 0.00 6.69 4.87 0.00 0.02 204580_at MMP12 31.87 10.07 0.00 0.00 25.18 9.61 0.00 0.00 28.72 10.32 0.00 0.00 4.50 8.80 0.01 0.09 160020_at MMP14 1.34 6.43 0.02 0.06 1.14 6.24 0.15 0.32 1.25 6.37 0.04 0.13 1.06 6.21 0.42 0.71 202827_s_at MMP14 1.69 5.99 0.01 0.03 1.30 5.68 0.19 0.38 1.50 5.91 0.04 0.12 1.13 5.57 0.45 0.73 202828_s_at MMP14 1.10 6.53 0.45 0.63 0.94 6.35 0.62 0.78 1.03 6.45 0.83 0.90 1.18 6.24 0.16 0.46 203365_s_at MMP15 0.76 6.83 0.07 0.17 0.77 6.86 0.06 0.17 0.77 6.80 0.06 0.15 0.90 7.04 0.37 0.67 204574_s_at MMP19 0.78 5.60 0.00 0.02 0.77 5.61 0.01 0.03 0.78 5.57 0.00 0.01 0.99 5.57 0.86 0.95 204575_s_at MMP19 2.19 5.52 0.00 0.01 1.95 5.35 0.02 0.08 2.08 5.54 0.01 0.02 1.69 5.03 0.03 0.19 227106_at MMP19 0.84 5.61 0.02 0.06 0.82 5.59 0.02 0.08 0.83 5.58 0.01 0.04 1.06 5.62 0.26 0.57 221953_s_at MMP24 /// 0.72 7.08 0.00 0.02 0.75 7.14 0.00 0.02 0.73 7.07 0.00 0.01 1.16 7.03 0.08 0.32 LOC729580 49679_s_at MMP24 /// 0.76 6.88 0.00 0.00 0.78 6.92 0.00 0.02 0.77 6.86 0.00 0.00 1.09 6.84 0.29 0.60 LOC729580 207890_s_at MMP25 1.39 5.70 0.00 0.01 1.22 5.54 0.05 0.15 1.31 5.66 0.01 0.03 1.31 5.63 0.06 0.27 219909_at MMP28 0.33 5.37 0.00 0.00 0.34 5.44 0.00 0.00 0.33 5.25 0.00 0.00 0.70 5.04 0.08 0.32 222937_s_at MMP28 0.57 6.10 0.00 0.00 0.55 6.09 0.00 0.00 0.56 6.02 0.00 0.00 0.91 5.86 0.38 0.68 224207_x_at MMP28 0.66 6.93 0.00 0.00 0.64 6.93 0.00 0.00 0.65 6.87 0.00 0.00 0.99 6.83 0.88 0.96 239272_at MMP28 0.47 6.33 0.00 0.00 0.55 6.54 0.00 0.00 0.50 6.33 0.00 0.00 1.01 6.11 0.94 0.98 239273_s_at MMP28 0.41 6.53 0.00 0.00 0.44 6.64 0.00 0.00 0.42 6.46 0.00 0.00 0.81 6.26 0.17 0.46 TIMP 201666_at TIMP1 13.82 10.06 0.00 0.00 9.13 9.45 0.00 0.00 11.51 10.12 0.00 0.00 5.71 8.92 0.00 0.00 genes 203167_at TIMP2 1.84 6.72 0.00 0.01 1.40 6.39 0.10 0.24 1.63 6.64 0.01 0.04 1.22 6.64 0.25 0.56 224560_at TIMP2 2.35 7.77 0.00 0.00 1.94 7.51 0.02 0.09 2.16 7.76 0.00 0.01 1.33 7.52 0.23 0.54 231579_s_at TIMP2 2.16 8.99 0.00 0.02 1.75 8.71 0.05 0.16 1.97 8.96 0.01 0.04 1.52 8.73 0.06 0.29 201147_s_at TIMP3 1.26 4.81 0.32 0.51 1.17 4.72 0.53 0.71 1.22 4.80 0.40 0.58 1.25 4.36 0.30 0.61 201148_s_at TIMP3 1.24 6.42 0.02 0.08 1.14 6.32 0.20 0.39 1.19 6.40 0.06 0.16 1.15 6.20 0.07 0.31 201149_s_at TIMP3 1.75 5.14 0.03 0.09 1.63 5.04 0.10 0.24 1.69 5.17 0.04 0.13 1.16 4.73 0.50 0.76 201150_s_at TIMP3 2.37 6.00 0.00 0.01 1.87 5.68 0.10 0.25 2.13 5.96 0.01 0.05 1.34 5.25 0.36 0.66 ADAM 205180_s_at ADAM8 1.30 5.75 0.13 0.27 1.20 5.65 0.22 0.42 1.25 5.73 0.16 0.31 1.09 5.76 0.64 0.85 genes 1555326_a_at ADAM9 2.44 7.68 0.00 0.00 1.75 7.26 0.04 0.12 2.10 7.59 0.00 0.01 1.34 6.80 0.21 0.51 202381_at ADAM9 2.18 9.93 0.00 0.00 1.83 9.69 0.00 0.02 2.01 9.92 0.00 0.00 1.66 9.45 0.00 0.01 202604_x_at ADAM10 0.81 6.77 0.09 0.22 0.70 6.62 0.04 0.12 0.76 6.66 0.06 0.15 0.75 6.38 0.04 0.23 214895_s_at ADAM10 0.76 6.72 0.07 0.18 0.72 6.68 0.14 0.32 0.74 6.66 0.10 0.23 0.57 6.44 0.00 0.03 1555896_a_at ADAM15 1.28 6.87 0.00 0.02 1.21 6.80 0.03 0.10 1.25 6.87 0.01 0.03 1.16 6.51 0.14 0.42 217007_s_at ADAM15 1.10 5.87 0.30 0.48 1.04 5.79 0.78 0.88 1.07 5.84 0.50 0.68 1.10 5.45 0.50 0.76 205745_x_at ADAM17 1.18 6.12 0.02 0.07 1.21 6.14 0.02 0.08 1.19 6.15 0.01 0.05 1.07 6.01 0.54 0.79 209765_at ADAM19 2.74 5.97 0.00 0.00 2.47 5.80 0.00 0.00 2.62 6.02 0.00 0.00 1.20 5.74 0.49 0.76 205997_at ADAM28 3.99 5.80 0.00 0.00 3.03 5.42 0.00 0.00 3.54 5.81 0.00 0.00 1.23 6.28 0.52 0.78 208269_s_at ADAM28 1.07 5.40 0.48 0.66 0.96 5.28 0.53 0.71 1.02 5.35 0.83 0.91 0.93 5.36 0.45 0.73 233868_x_at ADAM33 1.16 6.71 0.07 0.18 1.17 6.70 0.24 0.44 1.16 6.73 0.14 0.29 1.40 6.75 0.01 0.11 206134_at ADAMDEC1 0.93 8.05 0.82 0.90 1.43 8.52 0.10 0.25 1.13 8.28 0.66 0.80 0.42 9.17 0.00 0.05 222162_s_at ADAMTS1 4.42 5.47 0.00 0.00 3.45 5.11 0.00 0.02 3.96 5.50 0.00 0.00 1.90 4.85 0.03 0.18 235368_at ADAMTS5 1.74 5.32 0.00 0.01 1.65 5.23 0.01 0.06 1.70 5.35 0.00 0.02 1.34 5.81 0.04 0.23 220705_s_at ADAMTS7 0.84 5.47 0.10 0.23 0.83 5.47 0.12 0.28 0.83 5.45 0.10 0.23 1.11 5.56 0.35 0.65 226814_at ADAMTS9 3.68 6.37 0.00 0.00 2.63 5.93 0.00 0.00 3.17 6.33 0.00 0.00 1.85 5.34 0.00 0.04 220208_at ADAMTS13 0.89 5.74 0.24 0.42 0.93 5.78 0.30 0.50 0.91 5.75 0.24 0.41 0.90 5.62 0.21 0.52 Growth 212285_s_at AGRN 1.81 6.79 0.00 0.00 1.52 6.56 0.00 0.03 1.68 6.75 0.00 0.00 1.37 6.35 0.01 0.11 factor genes 217410_at AGRN 0.72 5.56 0.00 0.02 0.66 5.48 0.00 0.00 0.69 5.47 0.00 0.00 0.82 5.43 0.07 0.30 217419_x_at AGRN 1.50 6.58 0.00 0.00 1.31 6.41 0.04 0.14 1.42 6.55 0.00 0.02 1.35 6.10 0.01 0.11 202834_at AGT 3.03 5.76 0.00 0.00 2.28 5.38 0.00 0.00 2.67 5.72 0.00 0.00 0.33 6.06 0.00 0.00 213001_at ANGPTL2 2.99 6.33 0.00 0.00 2.80 6.19 0.00 0.01 2.90 6.41 0.00 0.00 2.02 5.84 0.02 0.15 213004_at ANGPTL2 1.83 4.88 0.01 0.06 1.79 4.82 0.01 0.04 1.81 4.94 0.01 0.04 1.74 4.47 0.00 0.07 221009_s_at ANGPTL4 2.10 6.20 0.00 0.00 1.40 5.71 0.05 0.16 1.75 6.06 0.00 0.02 0.84 6.26 0.36 0.66 223333_s_at ANGPTL4 2.04 5.34 0.00 0.00 1.55 5.00 0.01 0.05 1.81 5.27 0.00 0.01 0.86 5.48 0.46 0.73 205239_at AREG 4.11 8.45 0.00 0.00 2.89 7.98 0.00 0.01 3.52 8.41 0.00 0.00 2.09 5.94 0.08 0.33 210237_at ARTN 0.90 5.69 0.29 0.47 0.89 5.69 0.19 0.38 0.90 5.67 0.23 0.41 1.26 5.28 0.02 0.16 202701_at BMP1 0.74 6.13 0.00 0.01 0.78 6.19 0.01 0.03 0.76 6.12 0.00 0.01 1.02 5.96 0.77 0.91 205574_x_at BMP1 1.03 5.59 0.85 0.92 0.97 5.53 0.83 0.91 1.00 5.56 1.00 1.00 1.30 5.17 0.02 0.16 206725_x_at BMP1 1.00 5.41 0.97 0.99 0.93 5.32 0.42 0.62 0.97 5.36 0.72 0.84 1.18 5.27 0.07 0.31 207595_s_at BMP1 0.89 5.74 0.31 0.50 0.88 5.74 0.19 0.38 0.88 5.72 0.24 0.41 1.25 5.39 0.02 0.17 205289_at BMP2 1.01 8.94 0.95 0.97 0.91 8.83 0.50 0.69 0.96 8.88 0.80 0.88 0.60 7.73 0.03 0.17 205290_s_at BMP2 1.41 8.22 0.05 0.13 1.19 8.01 0.19 0.38 1.31 8.16 0.08 0.20 0.64 6.97 0.10 0.37 211518_s_at BMP4 1.01 5.59 0.94 0.97 0.90 5.47 0.41 0.61 0.96 5.53 0.72 0.83 0.95 5.42 0.50 0.77 211260_at BMP7 0.93 5.77 0.22 0.39 0.99 5.84 0.93 0.97 0.96 5.80 0.49 0.67 0.95 5.85 0.33 0.64 220203_at BMP8A 0.93 5.58 0.33 0.51 0.92 5.58 0.34 0.55 0.92 5.57 0.31 0.49 0.77 5.62 0.00 0.04 218529_at CD320 0.96 7.15 0.67 0.80 0.90 7.08 0.19 0.38 0.94 7.11 0.41 0.59 1.38 6.36 0.01 0.08 219505_at CECR1 3.64 7.03 0.00 0.00 3.05 6.76 0.00 0.00 3.37 7.07 0.00 0.00 1.43 6.42 0.23 0.55 219500_at CLCF1 1.17 5.64 0.08 0.19 1.01 5.47 0.91 0.95 1.10 5.57 0.32 0.51 1.01 5.31 0.91 0.97 207442_at CSF3 1.47 6.03 0.08 0.19 1.25 5.82 0.23 0.43 1.37 5.98 0.13 0.27 1.67 5.71 0.01 0.12 209101_at CTGF 3.04 7.50 0.00 0.00 2.31 7.13 0.00 0.02 2.70 7.47 0.00 0.00 1.81 5.97 0.03 0.18 205767_at EREG 2.83 6.71 0.01 0.04 1.62 6.03 0.23 0.43 2.22 6.51 0.04 0.12 0.87 4.94 0.78 0.91 218255_s_at FBRS 0.80 6.16 0.00 0.02 0.79 6.17 0.00 0.01 0.79 6.13 0.00 0.01 0.99 6.21 0.86 0.95 204421_s_at FGF2 1.63 5.11 0.00 0.02 1.46 4.96 0.02 0.08 1.55 5.11 0.01 0.03 1.24 4.68 0.09 0.33 208417_at FGF6 0.95 5.56 0.28 0.46 0.92 5.52 0.21 0.41 0.93 5.53 0.23 0.40 1.15 5.48 0.09 0.34 1554741_s_at FGF7 /// 4.16 4.66 0.00 0.00 3.68 4.45 0.00 0.01 3.94 4.75 0.00 0.00 1.80 4.12 0.09 0.34 KGFLP1 /// KGFLP2 206404_at FGF9 0.73 4.46 0.04 0.11 1.05 4.87 0.80 0.89 0.86 4.63 0.40 0.58 0.72 6.37 0.31 0.62 221136_at GDF2 0.73 5.97 0.00 0.01 0.70 5.94 0.00 0.00 0.71 5.91 0.00 0.00 0.87 5.94 0.13 0.41 206614_at GDF5 0.77 5.87 0.00 0.01 0.77 5.89 0.00 0.01 0.77 5.84 0.00 0.00 0.99 5.83 0.95 0.98 221577_x_at GDF15/// 1.54 6.50 0.06 0.15 1.30 6.29 0.31 0.52 1.43 6.45 0.10 0.22 0.99 5.67 0.97 0.99 LOC100287132 /// LOC100292463 202543_s_at GMFB 0.75 8.38 0.01 0.05 0.76 8.42 0.04 0.13 0.75 8.36 0.01 0.05 1.20 7.82 0.19 0.49 202544_at GMFB 0.65 8.83 0.00 0.00 0.72 8.96 0.00 0.00 0.68 8.83 0.00 0.00 0.98 8.77 0.80 0.92 204220_at GMFG 3.61 6.83 0.00 0.00 3.05 6.57 0.00 0.00 3.35 6.88 0.00 0.00 1.04 6.75 0.89 0.96 208308_s_at GPI 1.13 9.77 0.13 0.27 1.05 9.69 0.55 0.73 1.09 9.75 0.25 0.43 1.20 9.37 0.07 0.29 200678_x_at GRN 0.76 9.20 0.01 0.03 0.81 9.29 0.05 0.15 0.78 9.20 0.01 0.05 1.15 8.83 0.16 0.46 211284_s_at GRN 0.72 8.54 0.00 0.01 0.75 8.60 0.00 0.02 0.73 8.52 0.00 0.01 1.13 8.19 0.22 0.53 216041_x_at GRN 0.74 9.18 0.01 0.03 0.78 9.26 0.03 0.10 0.76 9.18 0.01 0.03 1.11 8.79 0.29 0.60 203821_at HBEGF 2.85 7.55 0.00 0.01 1.83 7.00 0.08 0.20 2.34 7.42 0.01 0.04 1.12 6.20 0.71 0.88 38037_at HBEGF 2.17 7.33 0.01 0.05 1.46 6.85 0.21 0.41 1.82 7.20 0.04 0.13 1.02 6.26 0.93 0.98 200896_x_at HDGF 0.91 9.40 0.13 0.27 0.83 9.31 0.00 0.01 0.88 9.34 0.02 0.07 0.89 9.58 0.23 0.54 216484_x_at HDGF 0.87 8.62 0.01 0.04 0.84 8.58 0.00 0.02 0.86 8.58 0.00 0.01 0.89 8.79 0.18 0.48 209524_at HDGFRP3 2.17 5.52 0.01 0.03 2.11 5.45 0.02 0.09 2.15 5.60 0.01 0.03 1.10 4.91 0.71 0.88 209526_s_at HDGFRP3 1.43 5.33 0.08 0.19 1.48 5.34 0.10 0.25 1.45 5.39 0.07 0.17 1.12 4.80 0.60 0.83 216693_x_at HDGFRP3 1.42 5.46 0.09 0.20 1.51 5.51 0.09 0.23 1.46 5.54 0.07 0.18 0.88 4.98 0.57 0.81 211577_s_at IGF1 0.91 5.64 0.30 0.49 0.90 5.62 0.08 0.21 0.91 5.62 0.18 0.34 0.96 5.58 0.61 0.83 202409_at IGF2 /// INS- 1.55 5.02 0.01 0.04 1.47 4.94 0.08 0.22 1.51 5.04 0.03 0.09 1.18 5.11 0.49 0.76 IGF2 210511_s_at INHBA 3.45 5.47 0.01 0.03 2.89 5.21 0.01 0.06 3.19 5.51 0.01 0.03 4.08 4.95 0.00 0.06 209098_s_at JAG1 1.42 6.68 0.04 0.12 1.17 6.45 0.47 0.66 1.30 6.61 0.16 0.32 0.86 5.65 0.50 0.77 209099_x_at JAG1 1.45 10.24 0.00 0.00 1.31 10.11 0.01 0.04 1.39 10.23 0.00 0.01 1.00 9.55 0.98 0.99 216268_s_at JAG1 1.55 10.23 0.00 0.00 1.41 10.10 0.00 0.02 1.49 10.23 0.00 0.00 1.00 9.49 0.98 0.99 231183_s_at JAG1 2.69 5.71 0.00 0.00 2.73 5.67 0.00 0.00 2.71 5.83 0.00 0.00 1.28 5.10 0.39 0.68 209784_s_at JAG2 0.94 5.42 0.54 0.71 0.83 5.29 0.08 0.21 0.89 5.35 0.23 0.41 0.89 5.64 0.34 0.64 32137_at JAG2 0.99 5.80 0.91 0.95 0.92 5.72 0.44 0.64 0.96 5.76 0.65 0.79 0.87 6.16 0.23 0.54 226534_at KITLG 0.51 7.79 0.00 0.00 0.74 8.24 0.02 0.09 0.60 7.92 0.00 0.01 1.39 7.52 0.05 0.25 206268_at LEFTY1 0.92 8.77 0.78 0.88 1.35 9.19 0.28 0.49 1.09 8.97 0.74 0.85 2.53 4.92 0.18 0.48 205266_at LIF 1.85 6.00 0.00 0.00 1.36 5.63 0.00 0.03 1.62 5.90 0.00 0.01 1.34 5.43 0.01 0.12 1559361_at MACC1 1.28 4.31 0.06 0.16 1.11 4.14 0.40 0.60 1.21 4.26 0.15 0.30 0.99 5.30 0.94 0.98 1566764_at MACC1 1.23 3.94 0.31 0.50 0.97 3.66 0.85 0.92 1.11 3.83 0.60 0.75 0.73 5.49 0.25 0.56 1566766_a_at MACC1 1.03 5.36 0.72 0.84 0.85 5.14 0.06 0.18 0.95 5.25 0.54 0.71 0.75 6.39 0.13 0.41 232151_at MACC1 1.02 5.06 0.85 0.92 0.89 4.91 0.35 0.56 0.96 4.99 0.76 0.86 0.67 6.33 0.06 0.27 202655_at MANF 2.47 9.12 0.00 0.00 2.16 8.92 0.00 0.00 2.33 9.14 0.00 0.00 1.51 8.60 0.00 0.05 209035_at MDK 1.66 7.79 0.02 0.08 1.87 7.89 0.01 0.05 1.75 7.92 0.01 0.03 0.70 8.70 0.04 0.23 206560_s_at MIA 1.66 6.05 0.03 0.10 1.48 5.89 0.02 0.07 1.58 6.04 0.02 0.08 1.45 5.74 0.05 0.25 205614_x_at MST1 0.86 6.31 0.12 0.26 0.84 6.29 0.21 0.41 0.85 6.28 0.14 0.28 1.07 7.47 0.74 0.90 216320_x_at MST1 0.78 6.37 0.02 0.08 0.74 6.34 0.08 0.20 0.76 6.32 0.03 0.10 0.99 7.67 0.94 0.98 214075_at NENF 1.09 5.87 0.35 0.53 1.12 5.90 0.09 0.23 1.11 5.90 0.21 0.38 1.12 5.72 0.13 0.42 218407_x_at NENF 1.08 7.85 0.24 0.42 1.11 7.87 0.19 0.38 1.09 7.87 0.17 0.32 1.19 7.72 0.02 0.13 208232_x_at NRG1 0.73 5.32 0.00 0.02 0.67 5.24 0.00 0.00 0.70 5.24 0.00 0.00 0.85 5.17 0.11 0.39 230329_s_at NUDT6 0.59 6.12 0.00 0.00 0.76 6.43 0.02 0.08 0.66 6.20 0.00 0.01 1.19 5.63 0.23 0.54 219475_at OSGIN1 0.73 5.47 0.00 0.02 0.68 5.42 0.00 0.01 0.71 5.40 0.00 0.01 0.80 5.93 0.13 0.41 214637_at OSM 1.32 5.22 0.12 0.26 1.14 5.05 0.40 0.61 1.24 5.17 0.21 0.38 1.42 5.11 0.11 0.37 230170_at OSM 2.54 5.07 0.01 0.03 1.70 4.57 0.10 0.24 2.13 4.95 0.03 0.08 2.49 4.70 0.03 0.18 205463_s_at PDGFA 0.86 7.05 0.20 0.37 0.87 7.07 0.13 0.30 0.86 7.04 0.16 0.31 0.89 7.22 0.36 0.66 216867_s_at PDGFA 0.99 5.16 0.96 0.98 0.97 5.14 0.79 0.89 0.98 5.15 0.89 0.94 0.88 5.37 0.47 0.74 229830_at PDGFA 0.73 7.81 0.06 0.16 0.83 7.96 0.09 0.22 0.77 7.84 0.07 0.17 0.87 8.12 0.37 0.67 216061_x_at PDGFB 1.00 5.57 0.96 0.98 0.90 5.47 0.17 0.36 0.95 5.52 0.51 0.68 1.08 5.41 0.37 0.67 218718_at PDGFC 1.32 5.27 0.22 0.39 1.32 5.26 0.15 0.32 1.32 5.30 0.17 0.33 0.66 6.52 0.03 0.19 225064_at RABEP1 0.94 6.47 0.52 0.69 0.90 6.42 0.36 0.56 0.92 6.44 0.41 0.60 0.86 6.44 0.09 0.35 225092_at RABEP1 0.96 6.88 0.68 0.81 0.86 6.76 0.29 0.50 0.92 6.81 0.44 0.62 0.75 6.96 0.03 0.18 219057_at RABEP2 0.76 5.60 0.00 0.01 0.74 5.59 0.00 0.00 0.75 5.55 0.00 0.00 1.09 5.64 0.30 0.61 74694_s_at RABEP2 0.84 6.35 0.08 0.19 0.94 6.49 0.50 0.69 0.88 6.40 0.19 0.36 1.07 6.54 0.45 0.73 77508_r_at RABEP2 0.84 6.47 0.03 0.10 0.84 6.48 0.03 0.10 0.84 6.45 0.02 0.08 1.04 6.45 0.59 0.82 209752_at REG1A 58.98 10.00 0.00 0.00 90.61 10.23 0.00 0.00 71.30 10.69 0.00 0.00 2.08 13.03 0.03 0.18 206286_s_at TDGF1 /// 0.89 5.88 0.59 0.75 0.96 5.96 0.84 0.92 0.92 5.91 0.68 0.81 0.84 5.03 0.37 0.67 TDGF3 205009_at TFF1 3.61 12.05 0.00 0.00 2.27 11.46 0.00 0.03 2.94 11.93 0.00 0.00 2.94 11.67 0.00 0.01 214476_at TFF2 3.11 7.37 0.00 0.00 2.10 6.88 0.03 0.11 2.62 7.28 0.00 0.01 4.06 7.53 0.02 0.17 204623_at TFF3 1.27 11.22 0.18 0.34 1.46 11.35 0.03 0.09 1.35 11.32 0.06 0.16 1.86 11.42 0.00 0.00 205016_at TGFA 0.44 7.54 0.00 0.00 0.46 7.65 0.00 0.00 0.45 7.48 0.00 0.00 0.69 7.61 0.01 0.08 211258_s_at TGFA 0.83 5.44 0.02 0.07 0.84 5.46 0.01 0.06 0.83 5.42 0.01 0.03 0.96 5.38 0.54 0.79 203085_s_at TGFB1 2.63 5.53 0.00 0.01 2.18 5.27 0.01 0.03 2.42 5.54 0.00 0.01 1.34 5.42 0.31 0.62 204858_s_at TYMP 2.49 7.09 0.00 0.00 2.18 6.90 0.00 0.00 2.35 7.12 0.00 0.00 1.46 7.17 0.01 0.08 210512_s_at VEGFA 1.23 9.32 0.11 0.24 0.98 9.06 0.90 0.95 1.12 9.21 0.39 0.58 0.91 9.35 0.37 0.67 210513_s_at VEGFA 0.94 6.71 0.60 0.76 0.71 6.42 0.02 0.08 0.83 6.55 0.18 0.35 0.85 6.56 0.18 0.48 211527_x_at VEGFA 1.19 6.31 0.17 0.33 0.86 5.95 0.32 0.52 1.03 6.15 0.83 0.90 0.77 6.14 0.04 0.22 212171_x_at VEGFA 0.96 7.38 0.67 0.80 0.76 7.12 0.00 0.02 0.87 7.24 0.14 0.29 0.90 7.23 0.25 0.56 209946_at VEGFC 1.79 4.74 0.00 0.01 1.73 4.67 0.01 0.03 1.76 4.79 0.00 0.01 1.56 4.71 0.04 0.23 205586_x_at VGF 0.79 5.42 0.01 0.04 0.72 5.33 0.00 0.00 0.76 5.34 0.00 0.00 0.96 5.31 0.59 0.82

Probe Set ID Gene Symbol UC R after therapy CDc R after therapy IBDc R after therapy CDi R after therapy (n=8) (n=11) (n=19) (n=8) vs vs vs vs control colons control colons control colons control ileums (n=6) (n=6) (n=6) (n=6) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 1.89 4.49 0.35 0.78 1.67 4.44 0.42 0.73 1.76 4.58 0.32 0.71 7.21 7.78 0.00 0.13 genes 201069_at MMP2 1.38 6.31 0.17 0.64 0.96 6.01 0.81 0.93 1.11 6.17 0.58 0.86 1.04 6.26 0.76 0.90 205828_at MMP3 1.28 4.54 0.60 0.90 1.26 4.56 0.67 0.88 1.27 4.60 0.60 0.87 2.82 4.61 0.04 0.28 204259_at MMP7 1.58 5.70 0.05 0.42 1.49 5.69 0.35 0.69 1.53 5.79 0.23 0.63 2.01 5.47 0.00 0.12 203936_s_at MMP9 1.36 5.36 0.22 0.69 1.33 5.37 0.31 0.66 1.34 5.43 0.23 0.63 0.47 5.57 0.04 0.29 205680_at MMP10 1.18 3.00 0.19 0.66 1.59 3.29 0.21 0.56 1.40 3.23 0.25 0.65 1.82 3.30 0.08 0.36 204580_at MMP12 2.31 6.76 0.09 0.52 2.20 6.80 0.16 0.50 2.24 6.95 0.10 0.45 0.56 6.69 0.22 0.54 160020_at MMP14 1.03 6.11 0.72 0.93 0.99 6.08 0.85 0.95 1.01 6.10 0.92 0.98 1.07 6.20 0.42 0.71 202827_s_at MMP14 1.17 5.52 0.13 0.59 1.11 5.49 0.38 0.71 1.14 5.53 0.21 0.61 0.94 5.38 0.72 0.89 202828_s_at MMP14 0.84 6.27 0.20 0.67 0.79 6.19 0.03 0.24 0.81 6.18 0.06 0.37 1.00 6.06 0.99 1.00 203365_s_at MMP15 0.91 7.06 0.12 0.57 0.95 7.09 0.59 0.83 0.93 7.06 0.33 0.72 1.26 7.35 0.04 0.28 204574_s_at MMP19 0.77 5.68 0.00 0.19 0.76 5.63 0.01 0.15 0.76 5.59 0.00 0.08 1.07 5.64 0.50 0.76 204575_s_at MMP19 1.04 4.64 0.61 0.90 1.13 4.73 0.05 0.31 1.09 4.71 0.18 0.57 1.05 4.50 0.55 0.79 227106_at MMP19 0.89 5.72 0.14 0.61 0.93 5.74 0.34 0.68 0.91 5.71 0.18 0.57 1.04 5.59 0.55 0.80 221953_s_at MMP24 /// 0.84 7.31 0.08 0.50 0.95 7.41 0.60 0.84 0.90 7.34 0.27 0.67 1.21 7.02 0.05 0.30 LOC729580 49679_s_at MMP24 /// 0.79 7.00 0.01 0.28 0.89 7.09 0.23 0.58 0.85 7.01 0.06 0.38 1.11 6.83 0.10 0.39 LOC729580 207890_s_at MMP25 0.99 5.31 0.91 0.98 1.01 5.33 0.86 0.95 1.00 5.33 0.96 0.99 0.92 5.27 0.25 0.57 219909_at MMP28 0.79 6.43 0.27 0.73 0.79 6.41 0.28 0.63 0.79 6.37 0.22 0.62 0.65 5.07 0.03 0.24 222937_s_at MMP28 0.77 6.53 0.04 0.40 0.83 6.58 0.20 0.55 0.81 6.51 0.06 0.38 0.91 5.89 0.30 0.62 224207_x_at MMP28 0.85 7.28 0.09 0.53 0.80 7.20 0.05 0.30 0.82 7.19 0.03 0.29 0.97 6.82 0.80 0.92 239272_at MMP28 0.88 7.10 0.43 0.83 0.93 7.14 0.60 0.84 0.91 7.10 0.47 0.81 0.87 5.98 0.54 0.79 239273_s_at MMP28 0.71 7.28 0.05 0.44 0.69 7.21 0.04 0.30 0.70 7.16 0.02 0.23 0.65 6.13 0.01 0.16 TIMP 201666_at TIMP1 3.27 8.00 0.01 0.23 2.65 7.94 0.02 0.20 2.90 8.19 0.00 0.11 1.79 7.51 0.01 0.20 genes 203167_at TIMP2 0.90 5.93 0.70 0.93 0.89 5.91 0.66 0.87 0.90 5.90 0.67 0.90 1.26 6.61 0.34 0.65 224560_at TIMP2 1.22 6.95 0.46 0.84 0.91 6.69 0.70 0.89 1.03 6.81 0.92 0.98 0.94 7.16 0.78 0.91 231579_s_at TIMP2 1.08 8.16 0.81 0.96 0.80 7.89 0.45 0.76 0.91 7.99 0.74 0.93 0.99 8.27 0.97 0.99 201147_s_at TIMP3 1.01 4.56 0.96 0.99 0.71 4.22 0.04 0.27 0.82 4.33 0.31 0.70 0.94 4.07 0.52 0.78 201148_s_at TIMP3 1.06 6.22 0.60 0.90 0.94 6.11 0.34 0.68 0.99 6.16 0.85 0.96 1.06 6.10 0.50 0.76 201149_s_at TIMP3 1.28 4.70 0.37 0.79 1.06 4.56 0.76 0.92 1.15 4.65 0.52 0.84 0.85 4.44 0.21 0.53 201150_s_at TIMP3 1.69 5.43 0.18 0.65 0.95 4.95 0.87 0.96 1.21 5.21 0.55 0.85 0.74 4.69 0.09 0.38 ADAM 205180_s_at ADAM8 0.78 5.25 0.02 0.34 0.75 5.18 0.01 0.17 0.77 5.15 0.00 0.12 0.76 5.44 0.04 0.28 genes 1555326_a_at ADAM9 1.03 6.67 0.92 0.98 1.01 6.66 0.98 0.99 1.02 6.67 0.95 0.99 1.08 6.55 0.81 0.93 202381_at ADAM9 1.27 9.23 0.19 0.66 1.37 9.32 0.10 0.41 1.33 9.34 0.09 0.44 1.53 9.25 0.01 0.20 202604_x_at ADAM10 0.67 6.69 0.06 0.46 0.63 6.58 0.01 0.16 0.65 6.54 0.02 0.21 0.72 6.42 0.05 0.30 214895_s_at ADAM10 0.63 6.66 0.09 0.52 0.66 6.65 0.05 0.30 0.65 6.56 0.05 0.35 0.57 6.57 0.04 0.28 1555896_a_at ADAM15 1.08 6.65 0.40 0.81 1.11 6.69 0.22 0.58 1.09 6.69 0.27 0.67 1.04 6.38 0.53 0.78 217007_s_at ADAM15 1.03 5.78 0.82 0.96 1.08 5.82 0.49 0.78 1.06 5.81 0.62 0.88 0.96 5.32 0.72 0.88 205745_x_at ADAM17 0.91 5.85 0.32 0.76 1.06 5.99 0.45 0.75 1.00 5.93 0.95 0.99 1.03 5.97 0.74 0.90 209765_at ADAM19 1.24 4.98 0.20 0.66 1.20 4.97 0.23 0.58 1.21 5.02 0.15 0.53 0.64 5.18 0.05 0.31 205997_at ADAM28 1.27 4.40 0.33 0.77 1.24 4.40 0.20 0.55 1.25 4.45 0.25 0.65 0.68 5.74 0.23 0.55 208269_s_at ADAM28 1.00 5.33 0.99 1.00 0.91 5.24 0.32 0.67 0.95 5.27 0.62 0.88 0.87 5.31 0.05 0.29 233868_x_at ADAM33 1.17 6.67 0.19 0.65 1.10 6.63 0.44 0.75 1.13 6.67 0.28 0.68 1.30 6.60 0.06 0.33 206134_at ADAMDEC1 1.11 8.22 0.75 0.94 0.79 7.90 0.54 0.81 0.91 8.03 0.79 0.94 0.35 9.24 0.00 0.11 222162_s_at ADAMTS1 3.56 4.80 0.00 0.17 2.13 4.46 0.01 0.13 2.65 4.82 0.00 0.12 0.89 4.06 0.54 0.79 235368_at ADAMTS5 1.04 4.71 0.68 0.92 1.07 4.74 0.58 0.83 1.06 4.74 0.59 0.87 1.07 5.55 0.46 0.74 220705_s_at ADAMTS7 0.88 5.57 0.28 0.74 0.85 5.52 0.14 0.47 0.86 5.51 0.17 0.56 1.26 5.63 0.08 0.36 226814_at ADAMTS9 1.57 5.24 0.00 0.12 1.38 5.16 0.06 0.33 1.46 5.28 0.01 0.19 1.11 4.76 0.42 0.71 220208_at ADAMTS13 0.90 5.78 0.23 0.69 0.87 5.74 0.08 0.37 0.88 5.73 0.07 0.39 1.05 5.77 0.54 0.79 Growth 212285_s_at AGRN 1.30 6.32 0.09 0.53 1.37 6.39 0.08 0.37 1.34 6.42 0.05 0.34 1.18 6.14 0.20 0.52 factor genes 217410_at AGRN 0.78 5.74 0.05 0.43 0.73 5.64 0.00 0.10 0.75 5.62 0.01 0.16 0.83 5.49 0.10 0.40 217419_x_at AGRN 1.12 6.20 0.38 0.80 1.18 6.26 0.29 0.63 1.15 6.26 0.29 0.69 1.26 5.97 0.05 0.31 202834_at AGT 1.06 4.53 0.60 0.90 1.18 4.63 0.30 0.65 1.13 4.61 0.39 0.76 0.28 6.21 0.00 0.03 213001_at ANGPTL2 1.31 5.29 0.11 0.56 1.00 5.06 0.99 1.00 1.12 5.19 0.40 0.77 0.99 5.07 0.93 0.97 213004_at ANGPTL2 0.94 4.14 0.50 0.86 0.94 4.13 0.48 0.77 0.94 4.12 0.43 0.78 1.13 3.97 0.21 0.53 221009_s_at ANGPTL4 0.80 5.16 0.06 0.45 1.00 5.35 0.99 1.00 0.91 5.24 0.52 0.83 0.98 6.42 0.91 0.97 223333_s_at ANGPTL4 0.97 4.49 0.77 0.95 1.09 4.60 0.52 0.80 1.04 4.56 0.76 0.94 1.05 5.69 0.83 0.94 205239_at AREG 3.84 7.93 0.01 0.21 3.84 8.08 0.00 0.04 3.84 8.30 0.00 0.04 1.36 5.39 0.56 0.80 210237_at ARTN 1.00 5.81 0.99 1.00 1.08 5.88 0.44 0.75 1.05 5.86 0.67 0.90 1.18 5.16 0.11 0.40 202701_at BMP1 0.78 6.27 0.04 0.39 0.82 6.29 0.02 0.22 0.81 6.23 0.01 0.20 1.05 5.98 0.59 0.82 205574_x_at BMP1 0.82 5.40 0.07 0.50 0.87 5.43 0.28 0.63 0.85 5.38 0.15 0.54 1.27 5.07 0.01 0.18 206725_x_at BMP1 0.96 5.37 0.68 0.92 0.99 5.39 0.90 0.97 0.97 5.38 0.80 0.95 1.20 5.24 0.10 0.39 207595_s_at BMP1 0.73 5.62 0.01 0.29 0.84 5.72 0.06 0.34 0.79 5.62 0.02 0.22 1.19 5.29 0.01 0.20 205289_at BMP2 1.08 8.99 0.72 0.93 1.17 9.08 0.22 0.58 1.13 9.06 0.44 0.79 0.71 8.00 0.09 0.37 205290_s_at BMP2 1.40 8.10 0.13 0.59 1.52 8.22 0.01 0.17 1.47 8.25 0.03 0.29 0.81 7.28 0.35 0.66 211518_s_at BMP4 1.27 5.78 0.12 0.58 0.87 5.45 0.16 0.50 1.02 5.60 0.88 0.97 0.93 5.42 0.40 0.70 211260_at BMP7 1.01 5.86 0.88 0.97 0.96 5.81 0.44 0.75 0.98 5.83 0.70 0.91 0.99 5.89 0.84 0.94 220203_at BMP8A 0.86 5.54 0.11 0.56 0.81 5.47 0.01 0.14 0.83 5.47 0.01 0.20 0.87 5.79 0.18 0.50 218529_at CD320 1.05 7.23 0.61 0.90 1.06 7.25 0.55 0.82 1.05 7.25 0.52 0.84 1.09 6.08 0.34 0.65 219505_at CECR1 1.45 5.84 0.13 0.59 1.25 5.74 0.51 0.80 1.33 5.85 0.29 0.68 0.77 5.82 0.39 0.69 219500_at CLCF1 1.04 5.49 0.74 0.94 1.02 5.48 0.78 0.92 1.03 5.49 0.74 0.93 1.03 5.33 0.68 0.87 207442_at CSF3 0.92 5.51 0.32 0.76 0.85 5.42 0.05 0.32 0.88 5.43 0.09 0.43 1.13 5.26 0.17 0.49 209101_at CTGF 2.02 6.79 0.02 0.33 1.61 6.66 0.07 0.36 1.77 6.84 0.02 0.25 0.88 5.22 0.55 0.80 205767_at EREG 1.71 5.95 0.33 0.77 1.88 6.09 0.11 0.43 1.81 6.15 0.17 0.56 0.60 4.67 0.14 0.45 218255_s_at FBRS 0.80 6.24 0.09 0.53 0.92 6.34 0.33 0.67 0.87 6.26 0.18 0.57 0.97 6.20 0.72 0.89 204421_s_at FGF2 1.06 4.59 0.47 0.84 1.02 4.57 0.86 0.95 1.03 4.59 0.69 0.91 1.19 4.58 0.10 0.39 208417_at FGF6 0.91 5.55 0.34 0.77 0.97 5.59 0.75 0.91 0.95 5.56 0.54 0.84 1.14 5.44 0.18 0.50 1554741_s_at FGF7 /// 1.67 3.44 0.00 0.18 1.56 3.43 0.01 0.16 1.60 3.54 0.00 0.11 1.05 3.53 0.73 0.89 KGFLP1 /// KGFLP2 206404_at FGF9 1.40 5.10 0.22 0.68 1.38 5.12 0.13 0.47 1.39 5.18 0.15 0.53 1.10 6.80 0.67 0.86 221136_at GDF2 0.87 6.23 0.35 0.79 0.75 6.07 0.01 0.14 0.80 6.09 0.06 0.36 0.92 6.01 0.47 0.74 206614_at GDF5 0.87 6.06 0.09 0.53 0.81 5.98 0.00 0.11 0.84 5.98 0.01 0.18 1.06 5.88 0.49 0.76 221577_x_at GDF15/// 2.94 6.89 0.04 0.40 1.85 6.58 0.12 0.44 2.25 6.89 0.05 0.36 0.76 5.46 0.28 0.60 LOC100287132 /// LOC100292463 202543_s_at GMFB 0.64 8.35 0.01 0.25 0.82 8.53 0.12 0.44 0.74 8.38 0.03 0.27 1.11 7.70 0.45 0.73 202544_at GMFB 0.85 9.18 0.02 0.30 0.87 9.19 0.04 0.30 0.86 9.16 0.02 0.21 1.06 8.84 0.49 0.76 204220_at GMFG 1.21 5.51 0.23 0.69 1.09 5.43 0.67 0.87 1.14 5.49 0.45 0.79 0.54 6.20 0.02 0.22 208308_s_at GPI 0.89 9.54 0.32 0.76 1.05 9.68 0.67 0.88 0.98 9.61 0.82 0.95 1.19 9.31 0.18 0.50 200678_x_at GRN 0.85 9.39 0.12 0.57 0.84 9.35 0.08 0.38 0.85 9.33 0.05 0.36 0.88 8.57 0.21 0.53 211284_s_at GRN 0.83 8.76 0.10 0.55 0.80 8.71 0.04 0.28 0.81 8.69 0.03 0.29 0.87 7.94 0.21 0.53 216041_x_at GRN 0.85 9.39 0.15 0.61 0.80 9.32 0.05 0.31 0.82 9.31 0.05 0.35 0.84 8.53 0.10 0.39 203821_at HBEGF 3.18 7.29 0.04 0.40 2.88 7.33 0.01 0.18 3.00 7.54 0.01 0.20 1.05 6.12 0.87 0.95 38037_at HBEGF 2.81 7.29 0.03 0.35 2.35 7.24 0.01 0.18 2.54 7.46 0.01 0.19 1.09 6.31 0.73 0.89 200896_x_at HDGF 0.77 9.29 0.00 0.18 0.86 9.37 0.03 0.23 0.82 9.29 0.01 0.14 0.96 9.67 0.67 0.86 216484_x_at HDGF 0.77 8.56 0.02 0.31 0.83 8.60 0.00 0.11 0.80 8.53 0.01 0.14 1.00 8.92 0.99 1.00 209524_at HDGFRP3 1.50 4.97 0.22 0.69 1.39 4.94 0.39 0.72 1.44 5.03 0.28 0.68 0.59 4.37 0.02 0.22 209526_s_at HDGFRP3 1.23 5.09 0.39 0.81 1.21 5.09 0.52 0.80 1.22 5.13 0.43 0.78 0.71 4.40 0.02 0.22 216693_x_at HDGFRP3 1.32 5.29 0.20 0.66 1.12 5.16 0.69 0.88 1.20 5.26 0.45 0.79 0.58 4.67 0.00 0.12 211577_s_at IGF1 0.99 5.73 0.87 0.97 0.85 5.59 0.05 0.30 0.91 5.63 0.20 0.60 0.91 5.55 0.36 0.67 202409_at IGF2 /// INS- 1.08 4.58 0.56 0.88 1.02 4.53 0.88 0.96 1.04 4.56 0.73 0.92 0.72 4.66 0.22 0.54 IGF2 210511_s_at INHBA 0.77 3.83 0.22 0.68 0.78 3.82 0.21 0.56 0.77 3.77 0.11 0.47 1.11 3.52 0.33 0.64 209098_s_at JAG1 0.83 6.13 0.45 0.83 1.08 6.35 0.71 0.90 0.97 6.24 0.88 0.97 0.90 5.73 0.68 0.87 209099_x_at JAG1 1.14 9.92 0.17 0.64 1.25 10.02 0.05 0.31 1.20 10.02 0.06 0.38 1.08 9.61 0.57 0.81 216268_s_at JAG1 1.20 9.88 0.07 0.48 1.34 10.00 0.02 0.22 1.28 10.00 0.02 0.23 1.07 9.55 0.62 0.84 231183_s_at JAG1 1.95 5.12 0.01 0.22 2.59 5.46 0.00 0.02 2.30 5.48 0.00 0.02 1.50 5.17 0.23 0.55 209784_s_at JAG2 0.93 5.43 0.57 0.88 0.74 5.21 0.01 0.18 0.82 5.27 0.08 0.41 0.92 5.69 0.54 0.79 32137_at JAG2 1.00 5.81 0.98 0.99 0.85 5.66 0.11 0.42 0.91 5.71 0.40 0.77 0.88 6.20 0.36 0.67 226534_at KITLG 0.89 8.48 0.36 0.79 0.82 8.38 0.18 0.53 0.85 8.39 0.23 0.63 0.98 7.15 0.94 0.98 206268_at LEFTY1 2.39 9.58 0.01 0.29 1.92 9.47 0.05 0.31 2.11 9.68 0.01 0.16 1.49 4.25 0.35 0.66 205266_at LIF 1.47 5.61 0.01 0.25 1.43 5.63 0.00 0.07 1.45 5.70 0.00 0.07 1.14 5.22 0.19 0.51 1559361_at MACC1 1.07 4.08 0.50 0.86 1.15 4.16 0.23 0.59 1.12 4.14 0.27 0.66 1.11 5.40 0.61 0.83 1566764_at MACC1 0.88 3.60 0.48 0.85 1.08 3.77 0.65 0.86 0.99 3.69 0.96 0.99 0.98 5.81 0.91 0.97 1566766_a_at MACC1 1.01 5.33 0.89 0.98 0.99 5.32 0.92 0.97 1.00 5.32 0.98 0.99 1.01 6.72 0.95 0.98 232151_at MACC1 1.23 5.21 0.23 0.69 1.04 5.07 0.68 0.88 1.12 5.16 0.39 0.76 0.91 6.69 0.64 0.85 202655_at MANF 1.38 8.34 0.03 0.36 1.58 8.50 0.00 0.06 1.49 8.51 0.00 0.08 1.37 8.41 0.09 0.38 209035_at MDK 1.10 7.28 0.75 0.94 0.97 7.18 0.92 0.97 1.02 7.23 0.92 0.98 0.87 8.96 0.43 0.72 206560_s_at MIA 1.30 5.68 0.07 0.48 1.14 5.59 0.14 0.48 1.20 5.67 0.08 0.41 1.09 5.41 0.56 0.80 205614_x_at MST1 1.36 6.74 0.26 0.72 0.99 6.48 0.96 0.99 1.13 6.63 0.58 0.86 1.53 7.75 0.04 0.27 216320_x_at MST1 1.22 6.83 0.51 0.86 0.90 6.57 0.60 0.84 1.02 6.69 0.94 0.99 1.40 7.97 0.09 0.38 214075_at NENF 1.09 5.84 0.48 0.85 1.23 5.96 0.01 0.18 1.17 5.94 0.10 0.46 1.05 5.64 0.50 0.76 218407_x_at NENF 1.22 7.92 0.07 0.48 1.22 7.94 0.02 0.23 1.22 7.97 0.01 0.20 1.12 7.63 0.14 0.45 208232_x_at NRG1 0.73 5.42 0.06 0.45 0.71 5.36 0.01 0.18 0.72 5.32 0.02 0.22 0.97 5.33 0.79 0.92 230329_s_at NUDT6 0.81 6.56 0.12 0.57 1.06 6.79 0.70 0.89 0.95 6.68 0.71 0.92 0.96 5.41 0.75 0.90 219475_at OSGIN1 0.74 5.59 0.03 0.35 0.76 5.58 0.04 0.28 0.75 5.52 0.02 0.23 1.10 6.26 0.47 0.75 214637_at OSM 0.97 4.88 0.83 0.96 0.96 4.87 0.65 0.87 0.97 4.87 0.73 0.93 1.21 4.90 0.04 0.26 230170_at OSM 0.81 3.82 0.04 0.39 0.78 3.77 0.03 0.24 0.79 3.74 0.02 0.24 1.14 3.82 0.52 0.78 205463_s_at PDGFA 1.15 7.35 0.23 0.69 1.05 7.27 0.77 0.92 1.09 7.33 0.53 0.84 0.89 7.26 0.53 0.78 216867_s_at PDGFA 1.15 5.28 0.36 0.79 1.32 5.43 0.09 0.40 1.25 5.41 0.17 0.56 0.97 5.48 0.88 0.96 229830_at PDGFA 1.22 8.33 0.16 0.62 1.02 8.19 0.90 0.97 1.10 8.27 0.56 0.85 0.85 8.13 0.43 0.72 216061_x_at PDGFB 0.89 5.48 0.36 0.79 0.90 5.48 0.27 0.62 0.90 5.46 0.27 0.66 1.01 5.33 0.94 0.98 218718_at PDGFC 0.99 4.95 0.98 0.99 0.87 4.82 0.57 0.82 0.92 4.86 0.73 0.92 0.45 6.32 0.01 0.16 225064_at RABEP1 0.90 6.45 0.37 0.80 0.81 6.33 0.07 0.36 0.84 6.35 0.12 0.49 0.73 6.35 0.03 0.24 225092_at RABEP1 0.83 6.77 0.25 0.71 0.81 6.72 0.20 0.55 0.82 6.70 0.18 0.57 0.70 6.97 0.03 0.25 219057_at RABEP2 0.80 5.73 0.02 0.32 0.85 5.76 0.06 0.33 0.83 5.71 0.02 0.25 1.01 5.56 0.92 0.97 74694_s_at RABEP2 0.81 6.38 0.17 0.64 0.96 6.52 0.64 0.86 0.89 6.43 0.35 0.73 0.98 6.45 0.88 0.96 77508_r_at RABEP2 0.97 6.64 0.75 0.94 0.89 6.56 0.08 0.38 0.92 6.58 0.33 0.71 1.09 6.47 0.24 0.56 209752_at REG1A 2.32 5.99 0.28 0.74 4.40 6.67 0.10 0.41 3.36 6.62 0.10 0.46 2.14 12.87 0.00 0.10 206286_s_at TDGF1 /// 1.43 6.31 0.23 0.70 1.35 6.30 0.26 0.61 1.39 6.37 0.19 0.59 0.76 4.99 0.15 0.47 TDGF3 205009_at TFF1 1.69 11.00 0.07 0.48 1.54 10.97 0.22 0.57 1.60 11.08 0.10 0.46 2.03 11.09 0.02 0.24 214476_at TFF2 1.17 6.19 0.22 0.69 1.41 6.39 0.13 0.46 1.30 6.35 0.15 0.54 2.29 6.70 0.06 0.31 204623_at TFF3 1.52 11.28 0.02 0.34 1.24 11.14 0.24 0.59 1.35 11.27 0.06 0.36 1.48 11.07 0.01 0.19 205016_at TGFA 0.50 7.92 0.00 0.15 0.62 8.05 0.00 0.11 0.57 7.87 0.00 0.07 0.83 7.85 0.11 0.41 211258_s_at TGFA 0.83 5.50 0.05 0.43 0.83 5.48 0.03 0.23 0.83 5.45 0.01 0.18 1.04 5.46 0.64 0.85 203085_s_at TGFB1 1.24 4.60 0.15 0.61 1.00 4.42 0.98 1.00 1.10 4.52 0.55 0.85 0.62 4.71 0.08 0.37 204858_s_at TYMP 1.04 6.08 0.82 0.96 1.17 6.19 0.35 0.69 1.12 6.16 0.49 0.82 1.18 6.90 0.23 0.55 210512_s_at VEGFA 0.99 9.06 0.96 0.99 1.03 9.10 0.90 0.97 1.01 9.08 0.97 0.99 1.10 9.53 0.41 0.70 210513_s_at VEGFA 0.75 6.55 0.11 0.56 0.77 6.54 0.05 0.30 0.76 6.48 0.06 0.37 0.95 6.69 0.75 0.90 211527_x_at VEGFA 0.87 6.00 0.34 0.78 0.83 5.93 0.23 0.58 0.84 5.93 0.23 0.63 0.89 6.33 0.43 0.72 212171_x_at VEGFA 0.81 7.25 0.08 0.52 0.79 7.20 0.05 0.31 0.80 7.18 0.05 0.34 0.98 7.33 0.89 0.96 209946_at VEGFC 1.25 4.25 0.01 0.28 1.10 4.16 0.22 0.58 1.16 4.23 0.06 0.36 1.08 4.29 0.47 0.74 205586_x_at VGF 0.72 5.42 0.01 0.20 0.77 5.45 0.01 0.15 0.75 5.37 0.00 0.10 1.05 5.40 0.59 0.82

Probe Set ID Gene Symbol UC NR after therapy CDc NR after therapy IBDc NR after CDi NR after therapy (n=16) (n=7) therapy (n=23) (n=10) vs vs vs vs control colons control colons control colons control ileums (n=6) (n=6) (n=6) (n=6) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 33.10 7.63 0.00 0.01 171.98 7.96 0.00 0.00 54.66 8.54 0.00 0.00 21.12 8.90 0.00 0.00 genes 201069_at MMP2 3.27 7.30 0.01 0.05 7.31 7.60 0.00 0.00 4.18 7.69 0.00 0.01 3.17 7.27 0.01 0.14 205828_at MMP3 26.61 7.78 0.00 0.01 128.46 8.11 0.00 0.00 42.97 8.64 0.00 0.00 24.92 6.65 0.00 0.04 204259_at MMP7 5.12 7.04 0.00 0.02 5.93 6.70 0.00 0.01 5.36 7.24 0.00 0.01 2.40 5.68 0.00 0.10 203936_s_at MMP9 3.51 6.42 0.01 0.04 8.32 6.75 0.00 0.00 4.56 6.84 0.00 0.01 0.94 6.13 0.88 0.96 205680_at MMP10 9.60 5.23 0.00 0.01 17.40 5.07 0.00 0.00 11.50 5.65 0.00 0.00 3.74 4.00 0.00 0.09 204580_at MMP12 17.14 9.05 0.00 0.00 36.29 8.86 0.00 0.00 21.54 9.58 0.00 0.00 2.51 8.00 0.11 0.45 160020_at MMP14 1.13 6.21 0.17 0.33 1.23 6.25 0.12 0.28 1.15 6.25 0.15 0.29 1.13 6.25 0.29 0.64 202827_s_at MMP14 1.30 5.66 0.13 0.27 1.57 5.74 0.06 0.18 1.38 5.75 0.09 0.21 1.20 5.60 0.33 0.67 202828_s_at MMP14 0.94 6.35 0.43 0.60 1.08 6.47 0.51 0.68 0.98 6.39 0.82 0.89 1.16 6.19 0.34 0.68 203365_s_at MMP15 0.78 6.88 0.01 0.05 0.73 6.89 0.01 0.05 0.77 6.83 0.01 0.03 1.19 7.31 0.23 0.59 204574_s_at MMP19 0.76 5.60 0.00 0.02 0.76 5.67 0.02 0.09 0.76 5.57 0.00 0.02 1.03 5.61 0.76 0.91 204575_s_at MMP19 2.09 5.39 0.00 0.03 3.39 5.56 0.00 0.00 2.42 5.63 0.00 0.01 1.62 4.90 0.06 0.36 227106_at MMP19 0.78 5.55 0.01 0.04 0.88 5.71 0.14 0.30 0.81 5.57 0.01 0.05 1.11 5.65 0.21 0.57 221953_s_at MMP24 /// 0.72 7.12 0.00 0.00 0.69 7.17 0.00 0.00 0.71 7.07 0.00 0.00 1.27 7.08 0.01 0.19 LOC729580 49679_s_at MMP24 /// 0.73 6.86 0.00 0.00 0.73 6.95 0.00 0.01 0.73 6.83 0.00 0.00 1.11 6.84 0.22 0.58 LOC729580 207890_s_at MMP25 1.26 5.56 0.01 0.04 1.49 5.63 0.00 0.03 1.32 5.64 0.00 0.02 1.37 5.62 0.04 0.28 219909_at MMP28 0.39 5.64 0.00 0.00 0.36 5.83 0.00 0.01 0.38 5.52 0.00 0.00 0.85 5.29 0.55 0.82 222937_s_at MMP28 0.60 6.21 0.00 0.01 0.52 6.23 0.00 0.01 0.57 6.11 0.00 0.00 1.08 6.03 0.56 0.83 224207_x_at MMP28 0.65 6.95 0.00 0.01 0.63 7.06 0.00 0.01 0.64 6.91 0.00 0.00 1.10 6.93 0.41 0.73 239272_at MMP28 0.51 6.50 0.00 0.01 0.45 6.59 0.00 0.03 0.49 6.40 0.00 0.00 1.12 6.20 0.59 0.84 239273_s_at MMP28 0.41 6.61 0.00 0.00 0.43 6.90 0.00 0.01 0.41 6.55 0.00 0.00 0.86 6.35 0.40 0.72 TIMP 201666_at TIMP1 8.89 9.32 0.00 0.00 12.88 9.01 0.00 0.00 9.95 9.66 0.00 0.00 5.57 8.58 0.00 0.02 genes 203167_at TIMP2 1.22 6.23 0.29 0.47 1.48 6.32 0.13 0.29 1.30 6.31 0.20 0.35 1.51 6.79 0.08 0.40 224560_at TIMP2 1.71 7.35 0.05 0.15 2.84 7.60 0.01 0.05 2.00 7.58 0.02 0.08 1.55 7.60 0.12 0.47 231579_s_at TIMP2 1.62 8.60 0.10 0.23 2.55 8.83 0.02 0.07 1.86 8.81 0.04 0.12 1.72 8.77 0.06 0.36 201147_s_at TIMP3 1.41 4.90 0.14 0.29 1.71 4.97 0.10 0.25 1.49 5.01 0.11 0.23 1.52 4.50 0.21 0.57 201148_s_at TIMP3 1.16 6.33 0.11 0.24 1.19 6.31 0.11 0.26 1.17 6.35 0.08 0.19 1.17 6.19 0.19 0.55 201149_s_at TIMP3 1.66 5.03 0.03 0.11 2.41 5.18 0.01 0.06 1.86 5.21 0.02 0.07 1.29 4.80 0.47 0.77 201150_s_at TIMP3 2.45 5.94 0.00 0.03 2.94 5.84 0.02 0.09 2.59 6.09 0.00 0.02 1.58 5.35 0.21 0.57 ADAM 205180_s_at ADAM8 1.21 5.65 0.12 0.26 1.64 5.83 0.01 0.07 1.33 5.77 0.06 0.15 1.12 5.77 0.56 0.82 genes 1555326_a_at ADAM9 2.00 7.37 0.01 0.05 1.48 6.95 0.20 0.38 1.82 7.34 0.02 0.08 0.95 6.44 0.86 0.95 202381_at ADAM9 2.06 9.79 0.00 0.00 1.61 9.40 0.02 0.08 1.91 9.77 0.00 0.00 1.42 9.22 0.06 0.34 202604_x_at ADAM10 0.74 6.70 0.06 0.16 0.69 6.73 0.04 0.13 0.73 6.65 0.04 0.11 0.64 6.28 0.02 0.21 214895_s_at ADAM10 0.74 6.72 0.09 0.22 0.68 6.74 0.05 0.16 0.72 6.66 0.06 0.15 0.45 6.32 0.01 0.17 1555896_a_at ADAM15 1.19 6.78 0.05 0.15 1.15 6.70 0.09 0.23 1.18 6.78 0.05 0.14 1.20 6.51 0.14 0.49 217007_s_at ADAM15 1.11 5.87 0.38 0.56 1.05 5.79 0.77 0.87 1.09 5.85 0.49 0.64 1.17 5.49 0.25 0.61 205745_x_at ADAM17 1.26 6.18 0.01 0.06 1.29 6.13 0.01 0.05 1.27 6.21 0.01 0.04 1.09 6.02 0.31 0.66 209765_at ADAM19 2.15 5.61 0.00 0.01 3.42 5.76 0.00 0.00 2.48 5.84 0.00 0.00 1.06 5.59 0.83 0.94 205997_at ADAM28 2.49 5.17 0.00 0.00 3.81 5.25 0.00 0.00 2.84 5.40 0.00 0.00 0.96 6.02 0.92 0.97 208269_s_at ADAM28 0.98 5.31 0.83 0.90 0.95 5.29 0.62 0.77 0.97 5.30 0.74 0.84 0.94 5.38 0.59 0.84 233868_x_at ADAM33 1.35 6.85 0.05 0.14 1.27 6.72 0.10 0.25 1.33 6.86 0.05 0.13 1.44 6.72 0.01 0.14 206134_at ADAMDEC1 0.87 7.98 0.56 0.71 1.06 8.17 0.85 0.92 0.92 8.04 0.74 0.84 0.32 9.09 0.00 0.10 222162_s_at ADAMTS1 5.51 5.55 0.00 0.00 7.46 5.32 0.00 0.00 6.04 5.81 0.00 0.00 2.11 4.82 0.09 0.41 235368_at ADAMTS5 1.53 5.13 0.02 0.06 2.01 5.22 0.00 0.01 1.66 5.26 0.00 0.02 1.91 6.07 0.03 0.27 220705_s_at ADAMTS7 0.85 5.51 0.14 0.29 0.84 5.54 0.13 0.30 0.85 5.49 0.12 0.25 1.18 5.59 0.18 0.54 226814_at ADAMTS9 3.35 6.13 0.00 0.00 3.38 5.81 0.00 0.00 3.36 6.25 0.00 0.00 2.04 5.32 0.06 0.34 220208_at ADAMTS13 0.89 5.75 0.11 0.25 0.88 5.77 0.19 0.37 0.89 5.74 0.08 0.19 0.92 5.66 0.28 0.64 Growth 212285_s_at AGRN 1.65 6.63 0.00 0.00 1.45 6.39 0.05 0.17 1.59 6.63 0.00 0.01 1.52 6.39 0.01 0.13 factor genes 217410_at AGRN 0.77 5.66 0.01 0.06 0.67 5.63 0.00 0.00 0.74 5.59 0.00 0.02 0.92 5.56 0.47 0.77 217419_x_at AGRN 1.27 6.36 0.02 0.07 1.13 6.20 0.42 0.61 1.23 6.34 0.07 0.17 1.47 6.12 0.00 0.11 202834_at AGT 2.38 5.39 0.00 0.02 1.94 5.00 0.00 0.00 2.24 5.40 0.00 0.01 0.28 6.11 0.00 0.01 213001_at ANGPTL2 2.46 6.01 0.01 0.03 4.28 6.19 0.00 0.01 2.91 6.29 0.00 0.01 2.22 5.80 0.01 0.18 213004_at ANGPTL2 1.64 4.71 0.05 0.14 2.13 4.77 0.00 0.03 1.78 4.85 0.02 0.07 1.83 4.41 0.02 0.21 221009_s_at ANGPTL4 1.46 5.75 0.01 0.05 1.15 5.46 0.34 0.54 1.36 5.70 0.04 0.11 0.99 6.44 0.97 0.99 223333_s_at ANGPTL4 1.51 4.95 0.01 0.04 1.42 4.79 0.02 0.10 1.48 4.97 0.01 0.03 0.90 5.55 0.55 0.82 205239_at AREG 4.94 8.50 0.00 0.00 4.11 7.92 0.00 0.01 4.67 8.58 0.00 0.00 2.26 5.88 0.10 0.44 210237_at ARTN 0.90 5.70 0.39 0.56 0.86 5.69 0.14 0.30 0.89 5.67 0.29 0.46 1.25 5.23 0.07 0.37 202701_at BMP1 0.73 6.14 0.00 0.00 0.78 6.28 0.02 0.08 0.74 6.13 0.00 0.00 1.11 6.03 0.32 0.67 205574_x_at BMP1 0.82 5.36 0.22 0.39 1.12 5.65 0.53 0.70 0.90 5.45 0.55 0.70 1.59 5.30 0.00 0.11 206725_x_at BMP1 0.88 5.27 0.16 0.32 1.11 5.48 0.33 0.53 0.94 5.34 0.56 0.71 1.32 5.34 0.01 0.15 207595_s_at BMP1 0.74 5.57 0.00 0.02 0.92 5.82 0.46 0.65 0.79 5.62 0.02 0.07 1.35 5.42 0.00 0.13 205289_at BMP2 1.01 8.93 0.97 0.99 0.86 8.81 0.24 0.43 0.96 8.88 0.76 0.85 0.60 7.83 0.01 0.19 205290_s_at BMP2 1.25 8.06 0.10 0.23 1.08 7.89 0.59 0.75 1.20 8.03 0.17 0.32 0.85 7.32 0.40 0.73 211518_s_at BMP4 0.88 5.45 0.15 0.31 0.90 5.50 0.37 0.57 0.88 5.44 0.17 0.32 0.91 5.40 0.38 0.71 211260_at BMP7 0.98 5.83 0.77 0.86 0.96 5.82 0.52 0.69 0.98 5.82 0.64 0.77 0.96 5.87 0.52 0.80 220203_at BMP8A 0.82 5.46 0.01 0.05 0.89 5.58 0.31 0.51 0.84 5.47 0.04 0.12 0.78 5.68 0.02 0.24 218529_at CD320 0.95 7.15 0.58 0.73 0.84 7.06 0.25 0.44 0.92 7.10 0.42 0.58 1.41 6.32 0.00 0.12 219505_at CECR1 2.79 6.61 0.00 0.01 4.00 6.61 0.00 0.02 3.11 6.84 0.00 0.00 1.18 6.18 0.62 0.85 219500_at CLCF1 1.12 5.57 0.22 0.39 1.04 5.49 0.76 0.87 1.09 5.56 0.38 0.55 1.00 5.31 0.98 0.99 207442_at CSF3 1.30 5.86 0.09 0.22 1.70 5.99 0.05 0.15 1.41 5.97 0.08 0.19 1.79 5.68 0.02 0.21 209101_at CTGF 2.97 7.36 0.00 0.00 3.96 7.28 0.00 0.01 3.24 7.56 0.00 0.00 1.92 5.91 0.10 0.42 205767_at EREG 3.26 6.74 0.00 0.03 4.07 6.59 0.00 0.03 3.48 6.93 0.00 0.01 0.90 4.99 0.85 0.95 218255_s_at FBRS 0.83 6.23 0.07 0.19 0.82 6.27 0.04 0.13 0.83 6.20 0.05 0.13 1.05 6.27 0.64 0.86 204421_s_at FGF2 1.48 4.96 0.03 0.10 1.69 4.96 0.00 0.01 1.54 5.04 0.01 0.04 1.26 4.65 0.15 0.50 208417_at FGF6 0.90 5.51 0.16 0.32 0.96 5.59 0.69 0.82 0.92 5.52 0.28 0.45 1.22 5.51 0.04 0.31 1554741_s_at FGF7 /// 4.19 4.52 0.00 0.01 6.48 4.47 0.00 0.01 4.78 4.81 0.00 0.00 2.06 4.13 0.10 0.43 KGFLP1 /// KGFLP2 206404_at FGF9 0.91 4.72 0.57 0.72 1.10 4.89 0.72 0.84 0.97 4.78 0.86 0.92 0.66 6.35 0.20 0.56 221136_at GDF2 0.75 6.04 0.01 0.06 0.72 6.08 0.00 0.03 0.74 6.00 0.00 0.02 0.90 5.98 0.25 0.61 206614_at GDF5 0.76 5.89 0.00 0.01 0.73 5.93 0.00 0.02 0.75 5.85 0.00 0.00 0.99 5.83 0.89 0.96 221577_x_at GDF15/// 2.04 6.75 0.03 0.10 1.60 6.37 0.19 0.37 1.89 6.73 0.03 0.10 0.77 5.45 0.32 0.67 LOC100287132 /// LOC100292463 202543_s_at GMFB 0.76 8.42 0.03 0.10 0.70 8.44 0.03 0.11 0.74 8.37 0.01 0.06 1.04 7.65 0.78 0.92 202544_at GMFB 0.71 8.95 0.00 0.00 0.67 9.01 0.00 0.01 0.70 8.90 0.00 0.00 0.98 8.77 0.77 0.92 204220_at GMFG 3.03 6.51 0.00 0.00 5.20 6.63 0.00 0.00 3.57 6.81 0.00 0.00 0.95 6.66 0.87 0.96 208308_s_at GPI 1.08 9.72 0.30 0.48 0.96 9.60 0.73 0.84 1.04 9.68 0.61 0.75 1.15 9.29 0.40 0.72 200678_x_at GRN 0.71 9.15 0.00 0.01 0.78 9.32 0.03 0.11 0.73 9.15 0.00 0.01 1.08 8.75 0.50 0.79 211284_s_at GRN 0.70 8.55 0.00 0.01 0.77 8.71 0.02 0.09 0.72 8.55 0.00 0.01 1.10 8.14 0.50 0.79 216041_x_at GRN 0.70 9.15 0.00 0.01 0.77 9.32 0.02 0.09 0.72 9.15 0.00 0.01 1.06 8.73 0.66 0.87 203821_at HBEGF 3.81 7.74 0.00 0.01 3.03 7.20 0.01 0.05 3.56 7.79 0.00 0.01 1.24 6.27 0.52 0.80 38037_at HBEGF 2.95 7.57 0.00 0.03 2.48 7.14 0.01 0.05 2.80 7.61 0.00 0.01 1.14 6.35 0.66 0.87 200896_x_at HDGF 0.91 9.41 0.06 0.17 0.88 9.40 0.12 0.27 0.90 9.39 0.06 0.15 0.97 9.68 0.69 0.88 216484_x_at HDGF 0.88 8.65 0.03 0.10 0.79 8.60 0.01 0.04 0.85 8.60 0.01 0.04 0.96 8.87 0.60 0.84 209524_at HDGFRP3 2.35 5.53 0.01 0.06 2.69 5.40 0.01 0.04 2.45 5.65 0.00 0.03 1.07 4.86 0.84 0.95 209526_s_at HDGFRP3 1.52 5.35 0.05 0.15 1.68 5.32 0.08 0.21 1.57 5.43 0.04 0.11 1.04 4.72 0.89 0.96 216693_x_at HDGFRP3 1.49 5.48 0.06 0.16 1.81 5.52 0.02 0.10 1.58 5.58 0.03 0.09 0.88 5.00 0.69 0.88 211577_s_at IGF1 0.88 5.61 0.10 0.24 0.97 5.72 0.71 0.83 0.91 5.63 0.17 0.32 0.85 5.48 0.07 0.37 202409_at IGF2 /// INS- 1.62 5.02 0.00 0.03 2.17 5.12 0.01 0.05 1.77 5.17 0.01 0.03 1.23 5.12 0.52 0.80 IGF2 210511_s_at INHBA 2.45 4.99 0.05 0.15 8.79 5.74 0.00 0.01 3.62 5.52 0.01 0.05 3.43 4.54 0.01 0.17 209098_s_at JAG1 1.33 6.57 0.13 0.28 1.17 6.40 0.45 0.64 1.28 6.56 0.19 0.34 0.79 5.60 0.39 0.72 209099_x_at JAG1 1.44 10.20 0.00 0.00 1.34 10.04 0.03 0.12 1.41 10.21 0.00 0.00 1.06 9.60 0.69 0.89 216268_s_at JAG1 1.56 10.19 0.00 0.00 1.45 10.01 0.01 0.05 1.52 10.21 0.00 0.00 1.05 9.53 0.76 0.91 231183_s_at JAG1 2.67 5.60 0.00 0.00 2.49 5.28 0.00 0.02 2.61 5.67 0.00 0.00 1.37 5.12 0.17 0.52 209784_s_at JAG2 0.93 5.42 0.53 0.69 0.97 5.47 0.81 0.89 0.94 5.43 0.58 0.72 1.02 5.77 0.91 0.97 32137_at JAG2 0.98 5.79 0.87 0.93 1.02 5.82 0.88 0.94 0.99 5.80 0.94 0.96 1.03 6.33 0.87 0.95 226534_at KITLG 0.64 8.09 0.00 0.01 0.62 8.19 0.01 0.04 0.63 8.04 0.00 0.01 1.29 7.39 0.12 0.46 206268_at LEFTY1 1.28 9.12 0.42 0.59 1.03 8.88 0.94 0.97 1.20 9.07 0.51 0.66 1.79 4.45 0.36 0.70 205266_at LIF 1.85 5.94 0.00 0.00 1.65 5.68 0.00 0.01 1.79 5.96 0.00 0.00 1.58 5.52 0.01 0.19 1559361_at MACC1 1.17 4.19 0.11 0.24 1.03 4.05 0.81 0.90 1.12 4.16 0.24 0.40 0.97 5.29 0.92 0.97 1566764_at MACC1 1.23 3.92 0.17 0.32 1.05 3.74 0.74 0.85 1.17 3.88 0.28 0.45 0.71 5.52 0.35 0.69 1566766_a_at MACC1 1.02 5.34 0.84 0.91 0.90 5.24 0.43 0.62 0.98 5.30 0.84 0.90 0.75 6.45 0.16 0.52 232151_at MACC1 1.10 5.14 0.32 0.50 0.94 4.98 0.59 0.74 1.05 5.09 0.64 0.77 0.68 6.42 0.14 0.49 202655_at MANF 2.36 8.98 0.00 0.00 2.41 8.76 0.00 0.00 2.38 9.06 0.00 0.00 1.51 8.52 0.02 0.24 209035_at MDK 1.37 7.53 0.16 0.31 1.76 7.64 0.10 0.24 1.48 7.65 0.08 0.20 0.74 8.80 0.23 0.59 206560_s_at MIA 1.38 5.81 0.03 0.10 1.85 5.95 0.00 0.03 1.51 5.94 0.01 0.05 1.28 5.56 0.33 0.68 205614_x_at MST1 0.79 6.25 0.07 0.19 0.69 6.21 0.02 0.08 0.76 6.18 0.02 0.08 1.24 7.59 0.34 0.68 216320_x_at MST1 0.72 6.32 0.02 0.08 0.63 6.31 0.01 0.05 0.69 6.24 0.00 0.02 1.16 7.82 0.58 0.83 214075_at NENF 1.19 5.96 0.02 0.08 1.18 5.90 0.08 0.22 1.19 5.97 0.02 0.08 1.19 5.76 0.11 0.44 218407_x_at NENF 1.10 7.86 0.18 0.35 1.12 7.85 0.29 0.48 1.11 7.88 0.15 0.29 1.15 7.66 0.14 0.48 208232_x_at NRG1 0.74 5.36 0.02 0.08 0.69 5.40 0.00 0.03 0.72 5.32 0.01 0.03 0.92 5.28 0.34 0.68 230329_s_at NUDT6 0.72 6.39 0.01 0.06 0.68 6.44 0.06 0.18 0.71 6.34 0.02 0.07 0.99 5.44 0.97 0.99 219475_at OSGIN1 0.70 5.46 0.00 0.03 0.72 5.58 0.02 0.08 0.70 5.43 0.00 0.02 0.95 6.13 0.68 0.88 214637_at OSM 1.26 5.15 0.19 0.35 2.05 5.46 0.00 0.02 1.46 5.34 0.06 0.16 1.46 5.08 0.04 0.30 230170_at OSM 2.10 4.77 0.02 0.07 5.49 5.32 0.00 0.00 2.81 5.18 0.01 0.03 2.67 4.60 0.02 0.21 205463_s_at PDGFA 0.88 7.09 0.40 0.58 0.86 7.11 0.26 0.45 0.87 7.07 0.34 0.51 0.98 7.34 0.92 0.97 216867_s_at PDGFA 0.88 5.04 0.21 0.38 0.92 5.11 0.49 0.67 0.89 5.04 0.27 0.44 1.07 5.56 0.76 0.92 229830_at PDGFA 0.84 7.98 0.38 0.56 0.77 7.96 0.06 0.18 0.82 7.93 0.26 0.43 0.92 8.19 0.63 0.86 216061_x_at PDGFB 0.94 5.51 0.46 0.63 0.93 5.52 0.45 0.64 0.94 5.50 0.40 0.56 1.16 5.47 0.22 0.58 218718_at PDGFC 1.29 5.22 0.27 0.44 1.84 5.42 0.02 0.07 1.43 5.36 0.11 0.23 0.65 6.58 0.11 0.45 225064_at RABEP1 0.95 6.48 0.52 0.68 0.94 6.49 0.57 0.73 0.94 6.47 0.48 0.64 0.74 6.34 0.07 0.37 225092_at RABEP1 1.04 6.96 0.73 0.83 0.97 6.90 0.82 0.90 1.02 6.94 0.89 0.93 0.78 7.04 0.05 0.32 219057_at RABEP2 0.77 5.64 0.00 0.03 0.75 5.69 0.04 0.13 0.77 5.61 0.01 0.03 1.13 5.66 0.10 0.42 74694_s_at RABEP2 0.88 6.43 0.20 0.37 0.90 6.48 0.45 0.64 0.89 6.42 0.27 0.44 1.08 6.54 0.49 0.78 77508_r_at RABEP2 0.80 6.44 0.02 0.07 0.80 6.49 0.00 0.03 0.80 6.41 0.01 0.03 1.12 6.51 0.23 0.58 209752_at REG1A 19.92 8.43 0.00 0.03 87.66 8.77 0.00 0.00 31.27 9.23 0.00 0.00 2.01 12.87 0.00 0.10 206286_s_at TDGF1 /// 1.15 6.16 0.53 0.69 0.87 5.90 0.57 0.73 1.06 6.07 0.79 0.87 0.73 4.93 0.12 0.46 TDGF3 205009_at TFF1 2.72 11.62 0.00 0.00 2.12 11.15 0.05 0.16 2.52 11.62 0.00 0.00 3.17 11.55 0.00 0.04 214476_at TFF2 1.89 6.73 0.01 0.06 2.12 6.65 0.07 0.19 1.96 6.83 0.03 0.09 5.24 7.51 0.01 0.16 204623_at TFF3 1.23 11.15 0.28 0.45 1.22 11.09 0.36 0.56 1.23 11.17 0.25 0.41 1.60 11.17 0.01 0.14 205016_at TGFA 0.41 7.55 0.00 0.00 0.46 7.89 0.00 0.01 0.42 7.51 0.00 0.00 0.68 7.67 0.01 0.20 211258_s_at TGFA 0.74 5.33 0.00 0.01 0.85 5.53 0.16 0.33 0.77 5.35 0.01 0.03 0.98 5.42 0.85 0.95 203085_s_at TGFB1 2.11 5.20 0.01 0.05 3.57 5.41 0.00 0.01 2.48 5.46 0.00 0.02 1.36 5.38 0.34 0.69 204858_s_at TYMP 1.97 6.75 0.00 0.01 2.67 6.80 0.00 0.00 2.16 6.92 0.00 0.00 1.58 7.17 0.01 0.18 210512_s_at VEGFA 1.22 9.28 0.29 0.47 0.93 9.01 0.64 0.78 1.12 9.21 0.51 0.66 0.96 9.41 0.73 0.90 210513_s_at VEGFA 0.83 6.60 0.10 0.23 0.62 6.42 0.01 0.06 0.76 6.48 0.05 0.13 0.81 6.55 0.13 0.47 211527_x_at VEGFA 0.98 6.09 0.87 0.92 0.80 5.94 0.13 0.29 0.92 6.01 0.55 0.70 0.73 6.14 0.08 0.39 212171_x_at VEGFA 0.88 7.29 0.15 0.30 0.75 7.19 0.00 0.03 0.84 7.22 0.05 0.13 0.81 7.16 0.02 0.24 209946_at VEGFC 1.85 4.72 0.00 0.00 2.86 4.88 0.00 0.00 2.11 4.93 0.00 0.00 1.62 4.66 0.11 0.44 205586_x_at VGF 0.78 5.43 0.01 0.06 0.70 5.41 0.00 0.01 0.76 5.37 0.00 0.02 1.00 5.35 0.98 1.00

Probe Set ID Gene Symbol UC after therapy CDc after therapy IBDc after therapy CDi after therapy (n=24) (n=18) (n=42) (n=18) vs vs vs vs UC before therapy CDc before therapy IBDc before therapy CDi before therapy (n=24) (n=18) (n=42) (n=18) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 0.15 8.98 0.00 0.01 0.11 8.87 0.00 0.02 0.14 8.93 0.00 0.00 0.59 10.24 0.05 0.34 genes 201069_at MMP2 0.60 7.72 0.03 0.15 0.54 7.58 0.00 0.12 0.57 7.66 0.00 0.01 0.67 7.46 0.00 0.08 205828_at MMP3 0.14 9.02 0.00 0.01 0.11 8.85 0.00 0.02 0.13 8.95 0.00 0.00 0.20 8.16 0.00 0.03 204259_at MMP7 0.32 7.93 0.00 0.01 0.49 7.19 0.00 0.13 0.38 7.61 0.00 0.00 0.68 6.32 0.01 0.14 203936_s_at MMP9 0.32 7.28 0.00 0.00 0.36 7.29 0.00 0.04 0.34 7.29 0.00 0.00 0.43 6.27 0.00 0.01 205680_at MMP10 0.22 6.21 0.00 0.00 0.32 5.69 0.00 0.08 0.26 5.98 0.00 0.00 0.41 4.90 0.00 0.10 204580_at MMP12 0.28 10.13 0.00 0.00 0.25 9.77 0.00 0.07 0.27 9.98 0.00 0.00 0.29 8.44 0.00 0.01 160020_at MMP14 0.82 6.36 0.00 0.01 0.92 6.25 0.14 0.58 0.86 6.31 0.00 0.00 1.04 6.26 0.48 0.79 202827_s_at MMP14 0.74 5.93 0.00 0.00 0.94 5.78 0.31 0.74 0.82 5.87 0.00 0.00 0.95 5.58 0.36 0.72 202828_s_at MMP14 0.82 6.41 0.00 0.01 0.92 6.30 0.09 0.50 0.86 6.37 0.00 0.00 0.92 6.24 0.13 0.50 203365_s_at MMP15 1.07 6.80 0.30 0.60 1.14 6.82 0.05 0.39 1.10 6.81 0.05 0.18 1.36 7.22 0.00 0.04 204574_s_at MMP19 0.98 5.52 0.68 0.86 0.98 5.50 0.74 0.94 0.98 5.51 0.60 0.80 1.06 5.61 0.22 0.60 204575_s_at MMP19 0.76 5.54 0.05 0.21 0.88 5.50 0.28 0.72 0.81 5.52 0.03 0.12 0.79 5.05 0.00 0.10 227106_at MMP19 0.97 5.54 0.43 0.71 1.12 5.59 0.02 0.27 1.03 5.56 0.23 0.48 1.02 5.65 0.62 0.87 221953_s_at MMP24 /// 1.05 7.02 0.30 0.60 1.12 7.12 0.06 0.43 1.08 7.06 0.04 0.17 1.07 7.13 0.09 0.43 LOC729580 49679_s_at MMP24 /// 0.98 6.79 0.65 0.85 1.08 6.86 0.08 0.48 1.02 6.82 0.37 0.63 1.02 6.88 0.70 0.90 LOC729580 207890_s_at MMP25 0.84 5.67 0.00 0.01 0.95 5.59 0.33 0.76 0.88 5.63 0.00 0.01 0.88 5.63 0.07 0.38 219909_at MMP28 1.47 5.33 0.00 0.03 1.75 5.44 0.00 0.10 1.59 5.38 0.00 0.00 1.08 4.97 0.50 0.81 222937_s_at MMP28 1.14 6.03 0.05 0.21 1.28 6.04 0.01 0.20 1.19 6.04 0.00 0.01 1.10 5.89 0.11 0.47 224207_x_at MMP28 1.08 6.86 0.14 0.40 1.15 6.86 0.03 0.34 1.11 6.86 0.01 0.07 1.06 6.86 0.30 0.68 239272_at MMP28 1.31 6.31 0.02 0.13 1.30 6.51 0.04 0.38 1.31 6.39 0.00 0.02 0.99 6.10 0.91 0.98 239273_s_at MMP28 1.20 6.40 0.06 0.24 1.32 6.55 0.01 0.19 1.25 6.47 0.00 0.02 0.94 6.13 0.44 0.77 TIMP 201666_at TIMP1 0.46 10.26 0.00 0.00 0.55 9.76 0.00 0.05 0.50 10.04 0.00 0.00 0.59 9.16 0.00 0.05 genes 203167_at TIMP2 0.60 6.53 0.00 0.01 0.79 6.31 0.01 0.24 0.68 6.43 0.00 0.00 1.14 6.80 0.20 0.58 224560_at TIMP2 0.65 7.71 0.01 0.09 0.75 7.49 0.03 0.33 0.69 7.61 0.00 0.01 0.93 7.57 0.50 0.81 231579_s_at TIMP2 0.65 8.91 0.02 0.13 0.73 8.65 0.03 0.31 0.69 8.79 0.00 0.02 0.89 8.79 0.21 0.59 201147_s_at TIMP3 1.00 4.88 1.00 1.00 0.86 4.65 0.24 0.69 0.94 4.78 0.50 0.73 0.98 4.42 0.84 0.95 201148_s_at TIMP3 0.91 6.41 0.05 0.21 0.90 6.28 0.10 0.50 0.91 6.36 0.01 0.06 0.98 6.23 0.62 0.87 201149_s_at TIMP3 0.87 5.20 0.16 0.44 0.87 5.15 0.28 0.72 0.87 5.18 0.09 0.26 0.93 4.73 0.33 0.70 201150_s_at TIMP3 0.91 6.18 0.50 0.76 0.81 5.71 0.13 0.57 0.87 5.98 0.15 0.38 0.84 5.23 0.25 0.63 ADAM 205180_s_at ADAM8 0.81 5.67 0.01 0.10 0.85 5.59 0.03 0.34 0.82 5.64 0.00 0.02 0.86 5.68 0.03 0.25 genes 1555326_a_at ADAM9 0.66 7.63 0.00 0.01 0.65 7.19 0.01 0.17 0.65 7.44 0.00 0.00 0.75 6.70 0.05 0.35 202381_at ADAM9 0.81 10.00 0.01 0.08 0.80 9.73 0.06 0.42 0.81 9.89 0.00 0.02 0.89 9.54 0.23 0.61 202604_x_at ADAM10 0.89 6.62 0.02 0.13 0.92 6.46 0.30 0.73 0.90 6.55 0.02 0.11 0.90 6.20 0.18 0.56 214895_s_at ADAM10 0.92 6.58 0.13 0.39 0.90 6.53 0.28 0.72 0.91 6.56 0.08 0.25 0.87 6.13 0.27 0.65 1555896_a_at ADAM15 0.90 6.87 0.00 0.04 0.93 6.82 0.14 0.57 0.91 6.85 0.00 0.02 0.97 6.54 0.49 0.80 217007_s_at ADAM15 0.98 5.88 0.71 0.88 1.01 5.84 0.89 0.98 0.99 5.86 0.87 0.95 0.98 5.47 0.74 0.92 205745_x_at ADAM17 0.96 6.14 0.43 0.71 0.97 6.15 0.59 0.89 0.96 6.14 0.34 0.60 1.00 6.04 0.94 0.98 209765_at ADAM19 0.65 5.95 0.00 0.01 0.73 5.88 0.02 0.27 0.69 5.92 0.00 0.00 0.71 5.55 0.00 0.05 205997_at ADAM28 0.50 5.70 0.00 0.00 0.65 5.46 0.00 0.14 0.56 5.60 0.00 0.00 0.67 6.07 0.00 0.11 208269_s_at ADAM28 0.93 5.37 0.09 0.31 0.97 5.24 0.60 0.89 0.95 5.31 0.10 0.29 0.97 5.31 0.58 0.85 233868_x_at ADAM33 1.11 6.83 0.06 0.26 1.02 6.74 0.78 0.95 1.07 6.79 0.13 0.34 0.98 6.86 0.73 0.91 206134_at ADAMDEC1 1.01 8.03 0.93 0.98 0.63 8.28 0.01 0.21 0.83 8.14 0.13 0.33 0.80 8.69 0.11 0.47 222162_s_at ADAMTS1 1.08 5.95 0.67 0.86 0.99 5.56 0.95 0.99 1.04 5.78 0.79 0.90 0.76 4.88 0.01 0.19 235368_at ADAMTS5 0.77 5.29 0.01 0.07 0.84 5.26 0.12 0.55 0.80 5.28 0.00 0.03 1.10 5.98 0.29 0.67 220705_s_at ADAMTS7 1.03 5.44 0.48 0.75 1.02 5.41 0.75 0.94 1.03 5.43 0.51 0.74 1.09 5.66 0.17 0.54 226814_at ADAMTS9 0.71 6.49 0.00 0.04 0.73 6.06 0.00 0.15 0.72 6.31 0.00 0.00 0.84 5.44 0.11 0.47 220208_at ADAMTS13 1.00 5.71 0.99 1.00 0.93 5.73 0.10 0.50 0.97 5.72 0.32 0.57 1.08 5.64 0.09 0.43 Growth 212285_s_at AGRN 0.84 6.83 0.01 0.08 0.94 6.63 0.29 0.73 0.88 6.75 0.01 0.05 0.99 6.46 0.84 0.95 factor genes 217410_at AGRN 1.08 5.52 0.16 0.43 1.07 5.39 0.20 0.65 1.07 5.46 0.06 0.20 1.07 5.40 0.27 0.65 217419_x_at AGRN 0.81 6.54 0.00 0.02 0.91 6.39 0.13 0.56 0.85 6.48 0.00 0.01 1.02 6.22 0.77 0.93 202834_at AGT 0.60 5.71 0.00 0.00 0.64 5.31 0.00 0.06 0.62 5.54 0.00 0.00 0.85 5.54 0.11 0.46 213001_at ANGPTL2 0.67 6.35 0.03 0.15 0.64 6.20 0.01 0.19 0.66 6.29 0.00 0.01 0.77 5.90 0.00 0.06 213004_at ANGPTL2 0.75 4.85 0.04 0.19 0.73 4.79 0.01 0.18 0.74 4.82 0.00 0.02 0.85 4.55 0.02 0.21 221009_s_at ANGPTL4 0.57 6.01 0.00 0.00 0.75 5.64 0.02 0.29 0.64 5.85 0.00 0.00 1.17 6.31 0.10 0.46 223333_s_at ANGPTL4 0.64 5.22 0.00 0.00 0.76 4.99 0.01 0.17 0.69 5.12 0.00 0.00 1.12 5.51 0.30 0.68 205239_at AREG 1.11 8.93 0.48 0.75 1.29 8.61 0.05 0.40 1.18 8.79 0.10 0.29 0.86 6.10 0.35 0.72 210237_at ARTN 1.03 5.69 0.63 0.84 1.11 5.72 0.16 0.60 1.06 5.70 0.21 0.45 0.97 5.34 0.55 0.83 202701_at BMP1 1.01 6.05 0.87 0.95 1.03 6.14 0.55 0.87 1.02 6.08 0.62 0.81 1.06 6.01 0.34 0.71 205574_x_at BMP1 0.80 5.44 0.01 0.07 1.00 5.50 0.95 0.99 0.88 5.46 0.03 0.12 1.10 5.33 0.18 0.56 206725_x_at BMP1 0.90 5.33 0.04 0.18 1.11 5.37 0.07 0.46 0.99 5.35 0.76 0.89 1.07 5.38 0.29 0.67 207595_s_at BMP1 0.83 5.58 0.00 0.03 0.99 5.68 0.89 0.98 0.90 5.62 0.01 0.05 1.02 5.48 0.70 0.90 205289_at BMP2 1.02 8.96 0.82 0.93 1.12 8.90 0.16 0.60 1.06 8.93 0.33 0.58 1.09 7.60 0.43 0.77 205290_s_at BMP2 0.92 8.26 0.38 0.67 1.11 8.16 0.21 0.66 1.00 8.22 0.98 0.99 1.31 7.00 0.02 0.22 211518_s_at BMP4 0.99 5.58 0.79 0.92 0.98 5.41 0.75 0.94 0.98 5.51 0.68 0.85 0.97 5.38 0.61 0.86 211260_at BMP7 1.06 5.79 0.08 0.29 0.97 5.80 0.54 0.87 1.02 5.80 0.37 0.63 1.02 5.84 0.60 0.86 220203_at BMP8A 0.90 5.48 0.00 0.05 0.91 5.49 0.08 0.46 0.90 5.49 0.00 0.01 1.07 5.57 0.23 0.62 218529_at CD320 1.02 7.16 0.62 0.83 1.07 7.10 0.23 0.68 1.04 7.13 0.23 0.48 0.91 6.41 0.12 0.48 219505_at CECR1 0.62 7.05 0.00 0.02 0.65 6.82 0.01 0.16 0.63 6.95 0.00 0.00 0.68 6.27 0.00 0.02 219500_at CLCF1 0.93 5.63 0.21 0.50 1.02 5.48 0.65 0.91 0.97 5.57 0.47 0.70 1.01 5.32 0.89 0.97 207442_at CSF3 0.79 5.96 0.02 0.12 0.87 5.83 0.13 0.56 0.82 5.91 0.01 0.04 0.87 5.80 0.08 0.42 209101_at CTGF 0.86 7.71 0.31 0.61 0.97 7.43 0.83 0.96 0.90 7.59 0.37 0.62 0.75 5.97 0.01 0.15 205767_at EREG 0.93 6.95 0.71 0.88 1.43 6.59 0.03 0.33 1.12 6.80 0.44 0.68 0.86 4.78 0.32 0.69 218255_s_at FBRS 1.03 6.12 0.59 0.82 1.11 6.16 0.04 0.37 1.06 6.13 0.11 0.30 1.02 6.22 0.59 0.85 204421_s_at FGF2 0.81 5.10 0.01 0.10 0.84 4.99 0.01 0.19 0.82 5.05 0.00 0.01 0.99 4.74 0.85 0.96 208417_at FGF6 0.95 5.51 0.18 0.45 1.05 5.54 0.42 0.81 0.99 5.52 0.85 0.94 1.03 5.55 0.54 0.83 1554741_s_at FGF7 /// 0.74 4.86 0.17 0.45 0.74 4.68 0.07 0.46 0.74 4.78 0.04 0.16 0.85 4.21 0.17 0.55 KGFLP1 /// KGFLP2 206404_at FGF9 1.43 4.63 0.00 0.01 1.18 5.04 0.10 0.51 1.32 4.81 0.00 0.00 1.15 6.35 0.04 0.31 221136_at GDF2 1.08 5.94 0.08 0.30 1.05 5.86 0.33 0.75 1.07 5.91 0.05 0.18 1.04 5.91 0.35 0.71 206614_at GDF5 1.04 5.82 0.31 0.61 1.02 5.81 0.63 0.91 1.03 5.81 0.25 0.50 1.02 5.85 0.63 0.87 221577_x_at GDF15/// 1.50 6.92 0.02 0.14 1.32 6.61 0.03 0.32 1.42 6.78 0.00 0.03 0.78 5.48 0.00 0.12 LOC100287132 /// LOC100292463 202543_s_at GMFB 0.96 8.26 0.40 0.69 1.00 8.34 0.99 1.00 0.98 8.30 0.60 0.80 0.89 7.80 0.12 0.48 202544_at GMFB 1.15 8.80 0.00 0.01 1.09 8.91 0.01 0.22 1.12 8.85 0.00 0.00 1.03 8.79 0.43 0.77 204220_at GMFG 0.62 6.85 0.00 0.04 0.65 6.66 0.02 0.26 0.63 6.77 0.00 0.00 0.71 6.52 0.00 0.06 208308_s_at GPI 0.90 9.73 0.03 0.18 0.96 9.68 0.50 0.85 0.93 9.71 0.04 0.17 0.97 9.41 0.60 0.86 200678_x_at GRN 0.99 9.11 0.86 0.95 1.03 9.20 0.62 0.90 1.01 9.15 0.84 0.93 0.86 8.77 0.02 0.24 211284_s_at GRN 1.03 8.47 0.55 0.79 1.06 8.53 0.24 0.69 1.04 8.50 0.22 0.47 0.88 8.14 0.05 0.35 216041_x_at GRN 1.00 9.10 0.95 0.98 1.03 9.16 0.62 0.90 1.01 9.13 0.70 0.86 0.86 8.72 0.03 0.27 203821_at HBEGF 1.26 8.02 0.20 0.49 1.52 7.59 0.02 0.30 1.36 7.84 0.02 0.10 1.03 6.26 0.78 0.93 38037_at HBEGF 1.34 7.77 0.10 0.32 1.58 7.37 0.01 0.21 1.43 7.60 0.00 0.04 1.09 6.33 0.27 0.65 200896_x_at HDGF 0.94 9.33 0.11 0.35 1.05 9.27 0.17 0.62 0.98 9.30 0.55 0.76 1.08 9.60 0.14 0.51 216484_x_at HDGF 0.97 8.56 0.38 0.67 0.98 8.49 0.50 0.85 0.97 8.53 0.26 0.51 1.10 8.81 0.04 0.32 209524_at HDGFRP3 0.93 5.70 0.60 0.82 0.83 5.61 0.30 0.74 0.89 5.66 0.28 0.53 0.75 4.73 0.00 0.12 209526_s_at HDGFRP3 0.99 5.43 0.91 0.97 0.91 5.44 0.46 0.84 0.96 5.43 0.56 0.77 0.78 4.67 0.00 0.10 216693_x_at HDGFRP3 1.01 5.57 0.93 0.98 0.88 5.58 0.30 0.73 0.95 5.58 0.54 0.76 0.84 4.80 0.01 0.15 211577_s_at IGF1 1.00 5.61 0.99 1.00 1.00 5.58 0.97 0.99 1.00 5.60 0.97 0.99 0.91 5.50 0.07 0.40 202409_at IGF2 /// INS- 0.91 5.08 0.33 0.63 0.97 4.99 0.82 0.96 0.94 5.04 0.40 0.64 0.82 5.03 0.12 0.49 IGF2 210511_s_at INHBA 0.48 5.31 0.01 0.06 0.66 5.35 0.03 0.31 0.55 5.33 0.00 0.01 0.51 4.97 0.00 0.04 209098_s_at JAG1 0.80 6.62 0.00 0.05 0.93 6.49 0.38 0.79 0.85 6.56 0.01 0.05 0.97 5.58 0.80 0.94 209099_x_at JAG1 0.92 10.29 0.06 0.25 0.97 10.19 0.62 0.90 0.94 10.25 0.08 0.25 1.07 9.60 0.40 0.75 216268_s_at JAG1 0.92 10.30 0.09 0.31 0.98 10.21 0.66 0.91 0.95 10.26 0.11 0.31 1.06 9.53 0.52 0.82 231183_s_at JAG1 0.89 5.91 0.10 0.33 0.94 5.96 0.38 0.79 0.91 5.93 0.07 0.23 1.12 5.27 0.43 0.77 209784_s_at JAG2 0.99 5.40 0.80 0.92 1.00 5.21 0.96 0.99 1.00 5.32 0.89 0.96 1.09 5.66 0.19 0.58 32137_at JAG2 1.00 5.79 0.96 0.99 1.00 5.68 0.95 0.99 1.00 5.74 1.00 1.00 1.10 6.18 0.21 0.59 226534_at KITLG 1.40 7.84 0.00 0.01 1.00 8.12 0.99 1.00 1.21 7.96 0.00 0.02 0.82 7.49 0.02 0.20 206268_at LEFTY1 1.71 9.13 0.00 0.01 1.14 9.36 0.28 0.72 1.44 9.23 0.00 0.01 0.65 4.95 0.08 0.41 205266_at LIF 0.93 6.13 0.28 0.58 1.10 5.82 0.21 0.66 1.00 6.00 0.95 0.98 1.02 5.55 0.77 0.93 1559361_at MACC1 0.88 4.29 0.05 0.21 0.99 4.17 0.91 0.98 0.93 4.24 0.12 0.32 1.05 5.33 0.71 0.90 1566764_at MACC1 0.90 3.92 0.16 0.43 1.11 3.72 0.40 0.80 0.98 3.83 0.83 0.92 1.12 5.46 0.47 0.79 1566766_a_at MACC1 0.99 5.36 0.73 0.89 1.13 5.17 0.06 0.41 1.05 5.27 0.22 0.46 1.15 6.38 0.06 0.36 232151_at MACC1 1.12 5.15 0.04 0.19 1.14 4.94 0.04 0.35 1.13 5.06 0.00 0.03 1.16 6.29 0.05 0.35 202655_at MANF 0.80 9.22 0.00 0.03 0.84 9.09 0.02 0.27 0.82 9.16 0.00 0.00 0.95 8.71 0.40 0.75 209035_at MDK 0.76 7.75 0.01 0.10 0.65 7.81 0.00 0.14 0.71 7.77 0.00 0.00 1.12 8.65 0.22 0.60 206560_s_at MIA 0.82 6.05 0.01 0.10 0.93 5.98 0.41 0.81 0.86 6.02 0.02 0.08 0.82 5.73 0.08 0.41 205614_x_at MST1 1.11 6.34 0.26 0.55 1.04 6.25 0.49 0.85 1.08 6.30 0.19 0.43 1.27 7.67 0.00 0.03 216320_x_at MST1 1.10 6.37 0.30 0.60 1.08 6.26 0.25 0.70 1.09 6.32 0.15 0.38 1.28 7.85 0.00 0.06 214075_at NENF 1.06 5.94 0.21 0.50 1.08 5.99 0.13 0.56 1.07 5.96 0.05 0.19 1.00 5.77 0.96 0.99 218407_x_at NENF 1.05 7.91 0.24 0.54 1.09 7.94 0.02 0.28 1.07 7.92 0.02 0.11 0.95 7.75 0.31 0.68 208232_x_at NRG1 1.01 5.23 0.90 0.96 1.03 5.15 0.52 0.86 1.02 5.20 0.61 0.81 1.12 5.19 0.03 0.26 230329_s_at NUDT6 1.28 6.14 0.00 0.01 1.17 6.46 0.03 0.34 1.23 6.28 0.00 0.00 0.82 5.56 0.03 0.26 219475_at OSGIN1 0.97 5.36 0.57 0.81 1.07 5.36 0.25 0.70 1.02 5.36 0.70 0.86 1.27 6.02 0.00 0.08 214637_at OSM 0.88 5.21 0.16 0.44 1.11 5.20 0.16 0.60 0.97 5.20 0.64 0.82 0.95 5.20 0.56 0.84 230170_at OSM 0.60 4.97 0.00 0.05 0.93 4.78 0.54 0.87 0.73 4.89 0.01 0.05 0.73 4.81 0.07 0.39 205463_s_at PDGFA 1.12 7.09 0.12 0.36 1.09 7.12 0.26 0.70 1.11 7.11 0.06 0.20 1.06 7.22 0.39 0.74 216867_s_at PDGFA 0.97 5.14 0.68 0.86 1.15 5.27 0.13 0.56 1.04 5.19 0.49 0.72 1.16 5.43 0.06 0.36 229830_at PDGFA 1.29 7.90 0.00 0.05 1.11 7.96 0.19 0.63 1.21 7.93 0.00 0.02 1.02 8.08 0.89 0.97 216061_x_at PDGFB 0.93 5.52 0.06 0.25 1.01 5.44 0.78 0.95 0.96 5.48 0.18 0.41 1.01 5.45 0.85 0.95 218718_at PDGFC 0.89 5.27 0.35 0.65 0.90 5.25 0.46 0.83 0.90 5.26 0.24 0.49 0.84 6.25 0.09 0.43 225064_at RABEP1 0.99 6.44 0.77 0.91 0.95 6.35 0.27 0.71 0.97 6.40 0.35 0.60 0.86 6.28 0.03 0.27 225092_at RABEP1 1.00 6.87 0.95 0.98 1.02 6.70 0.75 0.94 1.01 6.80 0.81 0.92 0.99 6.84 0.79 0.94 219057_at RABEP2 1.03 5.54 0.53 0.78 1.09 5.55 0.09 0.49 1.06 5.54 0.10 0.30 0.99 5.66 0.80 0.94 74694_s_at RABEP2 1.02 6.32 0.63 0.84 1.01 6.45 0.75 0.94 1.02 6.38 0.56 0.77 0.97 6.54 0.55 0.83 77508_r_at RABEP2 1.02 6.43 0.65 0.85 1.02 6.43 0.67 0.92 1.02 6.43 0.53 0.75 1.06 6.51 0.19 0.57 209752_at REG1A 0.16 9.87 0.00 0.00 0.16 10.43 0.00 0.11 0.16 10.11 0.00 0.00 0.99 13.29 0.96 0.99 206286_s_at TDGF1 /// 1.38 6.08 0.00 0.05 1.18 6.08 0.02 0.30 1.29 6.08 0.00 0.01 0.89 4.88 0.11 0.47 TDGF3 205009_at TFF1 0.64 12.10 0.00 0.00 0.75 11.57 0.09 0.49 0.69 11.87 0.00 0.00 0.88 11.97 0.35 0.72 214476_at TFF2 0.52 7.23 0.00 0.01 0.77 6.98 0.14 0.58 0.61 7.12 0.00 0.00 0.89 7.95 0.59 0.85 204623_at TFF3 1.03 11.31 0.69 0.87 0.86 11.35 0.12 0.54 0.96 11.33 0.49 0.72 0.83 11.51 0.01 0.19 205016_at TGFA 0.99 7.30 0.94 0.98 1.19 7.52 0.10 0.51 1.07 7.39 0.32 0.58 1.07 7.53 0.33 0.70 211258_s_at TGFA 0.92 5.33 0.13 0.39 1.00 5.41 0.92 0.98 0.95 5.36 0.18 0.42 1.05 5.40 0.40 0.75 203085_s_at TGFB1 0.67 5.53 0.01 0.06 0.78 5.31 0.03 0.31 0.72 5.44 0.00 0.01 0.71 5.28 0.00 0.12 204858_s_at TYMP 0.64 7.03 0.00 0.01 0.74 6.95 0.00 0.16 0.68 7.00 0.00 0.00 0.95 7.27 0.53 0.82 210512_s_at VEGFA 0.92 9.32 0.42 0.70 1.01 9.05 0.93 0.99 0.96 9.20 0.56 0.77 1.12 9.40 0.13 0.49 210513_s_at VEGFA 0.86 6.58 0.02 0.12 0.98 6.31 0.83 0.96 0.91 6.46 0.10 0.30 1.02 6.52 0.69 0.90 211527_x_at VEGFA 0.79 6.19 0.01 0.09 0.97 5.84 0.73 0.94 0.86 6.04 0.04 0.14 1.03 6.07 0.74 0.92 212171_x_at VEGFA 0.89 7.28 0.07 0.27 1.02 7.04 0.77 0.95 0.94 7.18 0.20 0.45 0.98 7.18 0.78 0.93 209946_at VEGFC 0.91 4.84 0.32 0.61 0.92 4.80 0.47 0.84 0.91 4.82 0.22 0.47 0.87 4.77 0.12 0.49 205586_x_at VGF 0.96 5.33 0.22 0.51 1.03 5.24 0.58 0.89 0.99 5.29 0.67 0.84 1.06 5.34 0.16 0.53

Probe Set ID Gene Symbol UC R after therapy CDc R after therapy IBDc R after therapy CDi R after therapy (n=8) (n=11) (n=19) (n=8) vs vs vs vs UC R before therapy CDc R before therapy IBDc R before CDi R before therapy (n=8) (n=11) therapy (n=19) (n=8) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 0.05 7.00 0.00 0.00 0.04 6.99 0.00 0.00 0.05 7.00 0.00 0.00 0.63 9.33 0.37 0.83 genes 201069_at MMP2 0.61 6.87 0.03 0.19 0.46 6.55 0.00 0.03 0.52 6.68 0.00 0.00 0.60 6.64 0.02 0.41 205828_at MMP3 0.05 6.85 0.00 0.00 0.04 7.04 0.00 0.00 0.04 6.96 0.00 0.00 0.15 6.62 0.02 0.45 204259_at MMP7 0.15 7.34 0.00 0.00 0.36 6.64 0.00 0.06 0.25 6.94 0.00 0.00 0.86 6.01 0.25 0.77 203936_s_at MMP9 0.27 6.49 0.00 0.00 0.27 6.46 0.00 0.01 0.27 6.47 0.00 0.00 0.39 5.77 0.01 0.33 205680_at MMP10 0.15 4.49 0.00 0.00 0.23 4.60 0.00 0.06 0.19 4.55 0.00 0.00 0.40 4.33 0.09 0.62 204580_at MMP12 0.12 8.83 0.00 0.00 0.11 8.79 0.00 0.01 0.11 8.81 0.00 0.00 0.19 7.53 0.00 0.28 160020_at MMP14 0.81 6.28 0.02 0.15 0.92 6.13 0.15 0.59 0.87 6.19 0.01 0.06 1.04 6.21 0.50 0.88 202827_s_at MMP14 0.79 5.79 0.00 0.04 1.00 5.54 0.98 1.00 0.91 5.64 0.11 0.34 0.90 5.42 0.26 0.77 202828_s_at MMP14 0.83 6.30 0.04 0.22 0.94 6.11 0.35 0.78 0.90 6.19 0.04 0.17 0.95 6.10 0.59 0.91 203365_s_at MMP15 0.94 7.04 0.31 0.67 1.15 6.97 0.08 0.47 1.05 7.00 0.33 0.63 1.37 7.26 0.00 0.31 204574_s_at MMP19 0.99 5.52 0.92 0.98 0.97 5.51 0.73 0.94 0.98 5.51 0.72 0.89 1.12 5.60 0.13 0.67 204575_s_at MMP19 0.73 4.90 0.00 0.02 0.87 4.89 0.08 0.46 0.81 4.89 0.00 0.01 0.79 4.70 0.03 0.47 227106_at MMP19 0.96 5.67 0.54 0.83 1.12 5.62 0.08 0.46 1.05 5.64 0.26 0.56 1.01 5.61 0.88 0.98 221953_s_at MMP24 /// 0.99 7.21 0.86 0.96 1.20 7.25 0.02 0.24 1.11 7.23 0.06 0.24 1.05 7.10 0.37 0.83 LOC729580 49679_s_at MMP24 /// 0.96 6.89 0.48 0.79 1.09 6.97 0.14 0.58 1.03 6.94 0.46 0.74 1.00 6.90 0.99 1.00 LOC729580 207890_s_at MMP25 0.79 5.48 0.02 0.16 0.90 5.42 0.12 0.55 0.85 5.44 0.01 0.06 0.77 5.41 0.01 0.36 219909_at MMP28 1.86 5.84 0.00 0.02 2.48 5.64 0.00 0.01 2.20 5.72 0.00 0.00 1.02 4.79 0.89 0.98 222937_s_at MMP28 1.31 6.18 0.01 0.08 1.56 6.16 0.00 0.01 1.45 6.17 0.00 0.00 1.05 5.79 0.48 0.87 224207_x_at MMP28 1.15 7.07 0.03 0.20 1.20 6.96 0.03 0.30 1.18 7.01 0.00 0.03 0.99 6.81 0.86 0.97 239272_at MMP28 1.73 6.63 0.00 0.02 1.68 6.72 0.00 0.02 1.70 6.68 0.00 0.00 0.97 5.92 0.82 0.97 239273_s_at MMP28 1.62 6.72 0.00 0.00 1.61 6.68 0.00 0.01 1.61 6.69 0.00 0.00 0.86 5.98 0.09 0.61 TIMP 201666_at TIMP1 0.30 9.60 0.00 0.00 0.46 9.00 0.00 0.03 0.39 9.25 0.00 0.00 0.48 8.40 0.01 0.37 genes 203167_at TIMP2 0.47 6.42 0.00 0.01 0.80 6.02 0.06 0.39 0.64 6.19 0.00 0.01 1.17 6.64 0.25 0.76 224560_at TIMP2 0.64 7.39 0.00 0.05 0.70 6.90 0.01 0.19 0.68 7.11 0.00 0.01 0.92 7.18 0.52 0.89 231579_s_at TIMP2 0.59 8.58 0.01 0.09 0.68 8.05 0.03 0.27 0.64 8.27 0.00 0.02 0.85 8.38 0.20 0.73 201147_s_at TIMP3 1.18 4.44 0.26 0.61 0.84 4.18 0.03 0.30 0.97 4.29 0.71 0.89 0.90 4.10 0.17 0.70 201148_s_at TIMP3 0.91 6.32 0.27 0.63 0.90 6.16 0.07 0.43 0.90 6.23 0.04 0.18 0.99 6.14 0.93 0.99 201149_s_at TIMP3 0.85 4.98 0.40 0.74 0.83 4.72 0.07 0.43 0.84 4.83 0.10 0.33 0.86 4.45 0.18 0.71 201150_s_at TIMP3 1.01 5.75 0.96 0.99 0.77 5.11 0.04 0.32 0.86 5.38 0.23 0.53 0.76 4.70 0.27 0.78 ADAM 205180_s_at ADAM8 0.78 5.28 0.02 0.15 0.77 5.22 0.00 0.06 0.77 5.25 0.00 0.00 0.82 5.42 0.08 0.60 genes 1555326_a_at ADAM9 0.42 7.31 0.00 0.00 0.60 7.03 0.01 0.12 0.51 7.15 0.00 0.00 0.81 6.75 0.29 0.79 202381_at ADAM9 0.56 9.80 0.00 0.00 0.81 9.63 0.20 0.65 0.69 9.70 0.00 0.02 0.94 9.56 0.55 0.89 202604_x_at ADAM10 0.82 6.59 0.01 0.06 0.92 6.41 0.43 0.83 0.87 6.49 0.06 0.24 0.98 6.23 0.84 0.97 214895_s_at ADAM10 0.84 6.50 0.09 0.35 0.94 6.48 0.63 0.91 0.90 6.49 0.21 0.51 1.01 6.22 0.97 0.99 1555896_a_at ADAM15 0.81 6.86 0.00 0.02 0.92 6.80 0.16 0.60 0.87 6.82 0.00 0.02 0.99 6.41 0.86 0.97 217007_s_at ADAM15 0.88 5.89 0.14 0.47 1.02 5.84 0.78 0.95 0.96 5.86 0.46 0.74 0.93 5.35 0.38 0.83 205745_x_at ADAM17 0.79 5.96 0.00 0.04 0.93 6.07 0.24 0.70 0.87 6.02 0.00 0.04 0.95 6.02 0.56 0.90 209765_at ADAM19 0.67 5.40 0.00 0.03 0.57 5.47 0.00 0.02 0.61 5.44 0.00 0.00 0.65 5.21 0.01 0.35 205997_at ADAM28 0.44 5.14 0.00 0.00 0.55 4.94 0.00 0.09 0.50 5.02 0.00 0.00 0.70 5.76 0.12 0.65 208269_s_at ADAM28 0.92 5.39 0.29 0.65 0.98 5.21 0.77 0.95 0.95 5.29 0.37 0.67 0.95 5.26 0.37 0.83 233868_x_at ADAM33 0.99 6.77 0.91 0.98 0.96 6.70 0.68 0.93 0.97 6.73 0.69 0.88 0.89 6.85 0.17 0.70 206134_at ADAMDEC1 1.64 7.92 0.12 0.43 0.55 8.22 0.02 0.25 0.87 8.09 0.55 0.80 0.79 8.76 0.26 0.77 222162_s_at ADAMTS1 1.32 5.39 0.25 0.61 1.00 4.85 0.98 1.00 1.12 5.08 0.48 0.75 0.72 4.23 0.03 0.48 235368_at ADAMTS5 0.74 4.95 0.00 0.06 0.80 4.94 0.01 0.20 0.78 4.94 0.00 0.01 0.96 5.63 0.69 0.94 220705_s_at ADAMTS7 0.98 5.51 0.78 0.93 1.03 5.42 0.74 0.95 1.01 5.46 0.87 0.96 1.10 5.70 0.32 0.81 226814_at ADAMTS9 0.54 5.96 0.00 0.00 0.65 5.64 0.00 0.04 0.60 5.77 0.00 0.00 0.76 5.01 0.04 0.50 220208_at ADAMTS13 0.92 5.77 0.19 0.53 0.91 5.74 0.05 0.37 0.91 5.75 0.01 0.09 1.15 5.70 0.08 0.60 Growth 212285_s_at AGRN 0.66 6.78 0.00 0.01 0.93 6.60 0.36 0.79 0.81 6.68 0.00 0.03 0.91 6.32 0.20 0.73 factor genes 217410_at AGRN 1.00 5.59 0.99 1.00 1.12 5.40 0.10 0.50 1.07 5.48 0.23 0.53 1.08 5.31 0.42 0.85 217419_x_at AGRN 0.65 6.59 0.00 0.00 0.89 6.43 0.12 0.55 0.78 6.49 0.00 0.01 1.01 6.11 0.91 0.99 202834_at AGT 0.47 5.12 0.00 0.00 0.61 5.07 0.00 0.05 0.55 5.09 0.00 0.00 0.92 5.49 0.58 0.91 213001_at ANGPTL2 0.78 5.64 0.05 0.25 0.59 5.45 0.00 0.03 0.66 5.53 0.00 0.00 0.74 5.28 0.05 0.52 213004_at ANGPTL2 0.82 4.24 0.03 0.20 0.75 4.32 0.00 0.07 0.78 4.28 0.00 0.01 0.84 4.17 0.03 0.48 221009_s_at ANGPTL4 0.44 5.62 0.00 0.00 0.82 5.49 0.22 0.67 0.63 5.55 0.00 0.01 1.14 6.31 0.44 0.86 223333_s_at ANGPTL4 0.52 4.94 0.00 0.04 0.78 4.83 0.05 0.35 0.66 4.87 0.00 0.01 1.19 5.59 0.38 0.83 205239_at AREG 1.04 8.73 0.86 0.96 1.10 8.69 0.49 0.86 1.08 8.71 0.58 0.82 0.84 5.71 0.44 0.86 210237_at ARTN 0.95 5.85 0.55 0.84 1.16 5.82 0.13 0.55 1.07 5.83 0.34 0.64 0.96 5.30 0.58 0.90 202701_at BMP1 1.02 6.10 0.81 0.94 1.10 6.12 0.12 0.54 1.07 6.11 0.22 0.51 1.02 5.99 0.78 0.96 205574_x_at BMP1 0.94 5.32 0.44 0.77 1.02 5.34 0.60 0.90 0.99 5.33 0.76 0.91 1.01 5.21 0.89 0.98 206725_x_at BMP1 0.94 5.39 0.41 0.75 1.10 5.32 0.25 0.71 1.03 5.35 0.65 0.86 1.03 5.33 0.67 0.93 207595_s_at BMP1 0.85 5.54 0.07 0.31 1.04 5.60 0.39 0.81 0.95 5.57 0.34 0.64 0.95 5.43 0.41 0.85 205289_at BMP2 0.97 9.06 0.84 0.95 1.24 9.00 0.05 0.35 1.12 9.03 0.23 0.53 1.28 7.62 0.08 0.60 205290_s_at BMP2 0.89 8.40 0.47 0.79 1.17 8.32 0.21 0.66 1.04 8.35 0.71 0.89 1.51 6.86 0.05 0.54 211518_s_at BMP4 1.16 5.82 0.15 0.47 1.00 5.38 0.95 0.99 1.07 5.56 0.29 0.59 0.98 5.40 0.79 0.96 211260_at BMP7 1.04 5.84 0.57 0.85 0.94 5.83 0.30 0.74 0.98 5.83 0.69 0.88 1.03 5.86 0.75 0.95 220203_at BMP8A 0.91 5.51 0.23 0.58 0.95 5.40 0.44 0.84 0.94 5.45 0.17 0.44 1.10 5.63 0.25 0.77 218529_at CD320 1.06 7.22 0.34 0.69 1.18 7.16 0.01 0.20 1.13 7.18 0.01 0.07 0.82 6.27 0.07 0.57 219505_at CECR1 0.63 6.40 0.03 0.17 0.52 6.33 0.00 0.05 0.56 6.36 0.00 0.00 0.60 6.03 0.00 0.30 219500_at CLCF1 0.89 5.60 0.31 0.66 1.05 5.45 0.33 0.77 0.98 5.51 0.78 0.92 1.04 5.32 0.40 0.84 207442_at CSF3 0.91 5.52 0.30 0.66 0.90 5.41 0.15 0.59 0.91 5.46 0.08 0.29 0.83 5.47 0.05 0.54 209101_at CTGF 0.93 7.28 0.64 0.88 0.82 7.04 0.30 0.74 0.87 7.14 0.28 0.58 0.74 5.37 0.02 0.43 205767_at EREG 0.95 6.31 0.90 0.97 1.26 6.25 0.19 0.64 1.12 6.27 0.56 0.81 1.07 4.30 0.69 0.94 218255_s_at FBRS 0.94 6.15 0.42 0.75 1.17 6.19 0.03 0.30 1.06 6.17 0.27 0.57 0.97 6.20 0.68 0.93 204421_s_at FGF2 0.83 4.76 0.07 0.32 0.89 4.66 0.10 0.50 0.86 4.71 0.02 0.10 1.12 4.61 0.18 0.71 208417_at FGF6 0.94 5.53 0.42 0.75 1.05 5.55 0.56 0.89 1.00 5.54 0.98 0.99 1.01 5.51 0.87 0.98 1554741_s_at FGF7 /// 0.88 3.86 0.35 0.70 0.72 3.89 0.06 0.40 0.78 3.88 0.05 0.20 0.84 3.69 0.39 0.84 KGFLP1 /// KGFLP2 206404_at FGF9 1.90 4.85 0.00 0.03 1.06 5.25 0.62 0.91 1.35 5.08 0.02 0.09 1.02 6.85 0.85 0.97 221136_at GDF2 1.17 6.03 0.10 0.39 1.03 5.90 0.65 0.92 1.09 5.95 0.14 0.40 1.06 5.92 0.36 0.82 206614_at GDF5 1.03 5.95 0.58 0.85 1.01 5.87 0.86 0.97 1.02 5.90 0.60 0.83 0.99 5.93 0.88 0.98 221577_x_at GDF15/// 2.10 7.03 0.03 0.19 1.42 6.64 0.05 0.35 1.67 6.80 0.01 0.05 0.74 5.51 0.03 0.46 LOC100287132 /// LOC100292463 202543_s_at GMFB 0.87 8.17 0.10 0.39 1.04 8.40 0.74 0.94 0.96 8.30 0.60 0.83 0.90 7.84 0.26 0.77 202544_at GMFB 1.23 8.93 0.01 0.07 1.12 9.04 0.01 0.15 1.16 9.00 0.00 0.00 1.09 8.81 0.11 0.64 204220_at GMFG 0.47 6.17 0.00 0.01 0.49 5.98 0.00 0.04 0.48 6.06 0.00 0.00 0.65 6.12 0.03 0.45 208308_s_at GPI 0.75 9.68 0.00 0.05 1.02 9.69 0.81 0.96 0.89 9.68 0.06 0.25 0.97 9.43 0.74 0.95 200678_x_at GRN 1.00 9.29 0.98 1.00 1.08 9.21 0.32 0.76 1.04 9.24 0.43 0.72 0.84 8.62 0.04 0.52 211284_s_at GRN 1.02 8.64 0.84 0.95 1.11 8.52 0.15 0.58 1.07 8.57 0.21 0.50 0.83 7.99 0.03 0.47 216041_x_at GRN 1.02 9.28 0.84 0.95 1.07 9.16 0.40 0.82 1.05 9.21 0.44 0.73 0.81 8.58 0.02 0.43 203821_at HBEGF 1.31 7.81 0.20 0.55 1.26 7.70 0.28 0.73 1.28 7.75 0.12 0.37 1.04 6.12 0.76 0.95 38037_at HBEGF 1.46 7.66 0.03 0.18 1.34 7.46 0.18 0.62 1.39 7.54 0.03 0.15 1.15 6.26 0.06 0.56 200896_x_at HDGF 0.80 9.28 0.00 0.05 1.03 9.27 0.50 0.86 0.93 9.27 0.09 0.30 1.07 9.60 0.44 0.86 216484_x_at HDGF 0.84 8.51 0.03 0.19 0.97 8.52 0.53 0.87 0.92 8.52 0.03 0.16 1.13 8.83 0.10 0.63 209524_at HDGFRP3 1.16 5.11 0.28 0.64 0.86 5.21 0.54 0.88 0.98 5.17 0.89 0.96 0.68 4.33 0.02 0.44 209526_s_at HDGFRP3 1.25 5.05 0.07 0.31 1.00 5.19 0.97 0.99 1.10 5.13 0.36 0.66 0.71 4.43 0.00 0.30 216693_x_at HDGFRP3 1.45 5.19 0.01 0.09 0.94 5.27 0.68 0.93 1.13 5.24 0.30 0.61 0.74 4.56 0.00 0.31 211577_s_at IGF1 1.09 5.66 0.22 0.58 0.98 5.52 0.65 0.92 1.03 5.58 0.51 0.77 1.02 5.47 0.73 0.94 202409_at IGF2 /// INS- 0.85 4.75 0.20 0.54 0.97 4.57 0.68 0.93 0.92 4.64 0.23 0.53 0.63 4.79 0.01 0.38 IGF2 210511_s_at INHBA 0.56 4.08 0.01 0.08 0.48 4.22 0.00 0.04 0.51 4.16 0.00 0.00 0.44 4.18 0.02 0.42 209098_s_at JAG1 0.66 6.32 0.00 0.04 0.89 6.47 0.25 0.70 0.78 6.40 0.01 0.05 1.21 5.52 0.22 0.75 209099_x_at JAG1 0.80 10.17 0.00 0.06 0.94 10.18 0.25 0.70 0.88 10.17 0.00 0.04 1.26 9.50 0.03 0.46 216268_s_at JAG1 0.80 10.15 0.00 0.06 0.94 10.19 0.33 0.77 0.88 10.18 0.01 0.06 1.25 9.43 0.03 0.49 231183_s_at JAG1 0.82 5.68 0.02 0.16 0.90 6.01 0.14 0.57 0.87 5.87 0.01 0.06 1.44 5.16 0.13 0.67 209784_s_at JAG2 0.90 5.47 0.08 0.35 0.97 5.08 0.65 0.92 0.94 5.24 0.18 0.47 0.98 5.65 0.84 0.97 32137_at JAG2 0.93 5.87 0.31 0.66 1.04 5.55 0.46 0.85 0.99 5.68 0.87 0.96 1.01 6.11 0.92 0.99 226534_at KITLG 1.65 8.04 0.00 0.05 1.06 8.24 0.53 0.88 1.27 8.15 0.01 0.09 0.76 7.33 0.04 0.51 206268_at LEFTY1 2.04 9.60 0.00 0.02 1.30 9.61 0.12 0.54 1.57 9.61 0.00 0.02 0.79 4.67 0.17 0.71 205266_at LIF 1.06 5.81 0.62 0.87 1.06 5.77 0.46 0.84 1.06 5.79 0.39 0.69 0.90 5.38 0.20 0.73 1559361_at MACC1 0.93 4.17 0.37 0.72 1.07 4.18 0.48 0.86 1.01 4.18 0.94 0.98 0.96 5.50 0.80 0.96 1566764_at MACC1 0.86 3.63 0.14 0.46 1.20 3.68 0.24 0.69 1.04 3.66 0.70 0.88 1.16 5.70 0.54 0.89 1566766_a_at MACC1 0.99 5.35 0.91 0.97 1.20 5.18 0.01 0.18 1.11 5.25 0.08 0.30 1.29 6.54 0.06 0.55 232151_at MACC1 1.29 5.15 0.01 0.09 1.24 4.94 0.01 0.17 1.26 5.03 0.00 0.01 1.33 6.43 0.02 0.44 202655_at MANF 0.59 8.93 0.00 0.01 0.74 8.95 0.00 0.08 0.67 8.94 0.00 0.00 0.91 8.67 0.34 0.81 209035_at MDK 0.54 7.79 0.00 0.04 0.50 7.67 0.00 0.01 0.51 7.72 0.00 0.00 1.27 8.70 0.03 0.47 206560_s_at MIA 0.71 6.09 0.04 0.24 0.82 5.80 0.09 0.48 0.77 5.92 0.01 0.08 1.03 5.44 0.82 0.96 205614_x_at MST1 1.46 6.66 0.07 0.31 1.03 6.46 0.71 0.94 1.19 6.54 0.10 0.33 1.16 7.91 0.02 0.44 216320_x_at MST1 1.37 6.72 0.16 0.49 1.05 6.48 0.62 0.91 1.17 6.58 0.17 0.45 1.20 8.05 0.06 0.56 214075_at NENF 1.06 5.85 0.49 0.80 1.11 5.99 0.11 0.53 1.09 5.93 0.10 0.33 0.94 5.71 0.28 0.79 218407_x_at NENF 1.10 7.97 0.21 0.57 1.10 7.98 0.05 0.38 1.10 7.97 0.02 0.13 1.01 7.69 0.88 0.98 208232_x_at NRG1 0.93 5.28 0.37 0.72 1.04 5.16 0.64 0.92 0.99 5.21 0.86 0.95 1.15 5.21 0.10 0.63 230329_s_at NUDT6 1.35 6.21 0.00 0.06 1.29 6.64 0.01 0.17 1.31 6.46 0.00 0.01 0.84 5.52 0.12 0.66 219475_at OSGIN1 0.93 5.46 0.33 0.69 1.15 5.34 0.07 0.42 1.05 5.39 0.38 0.68 1.32 6.12 0.04 0.50 214637_at OSM 0.94 4.90 0.57 0.84 1.03 4.82 0.53 0.88 0.99 4.86 0.91 0.97 1.04 4.98 0.62 0.92 230170_at OSM 0.46 4.24 0.00 0.01 0.73 3.87 0.00 0.03 0.60 4.03 0.00 0.00 0.67 4.20 0.10 0.62 205463_s_at PDGFA 1.17 7.32 0.04 0.23 1.18 7.18 0.13 0.56 1.18 7.24 0.02 0.13 0.97 7.21 0.79 0.96 216867_s_at PDGFA 0.97 5.39 0.83 0.95 1.28 5.39 0.05 0.38 1.14 5.39 0.20 0.49 1.08 5.40 0.42 0.85 229830_at PDGFA 1.41 8.20 0.00 0.05 1.23 8.05 0.08 0.46 1.31 8.11 0.00 0.03 0.94 8.07 0.73 0.94 216061_x_at PDGFB 0.94 5.46 0.41 0.75 1.05 5.40 0.41 0.82 1.00 5.42 0.99 1.00 1.00 5.34 0.98 1.00 218718_at PDGFC 1.24 4.79 0.35 0.70 0.78 4.93 0.15 0.58 0.95 4.87 0.71 0.89 0.75 6.03 0.14 0.67 225064_at RABEP1 1.04 6.36 0.61 0.86 0.99 6.23 0.88 0.98 1.01 6.28 0.83 0.94 0.88 6.25 0.10 0.63 225092_at RABEP1 0.96 6.68 0.65 0.88 1.03 6.60 0.72 0.94 1.00 6.63 0.97 0.99 0.99 6.75 0.94 0.99 219057_at RABEP2 0.97 5.61 0.61 0.86 1.12 5.60 0.10 0.49 1.06 5.60 0.26 0.57 0.95 5.60 0.47 0.87 74694_s_at RABEP2 1.03 6.22 0.75 0.92 1.04 6.46 0.38 0.80 1.04 6.36 0.47 0.74 0.94 6.48 0.39 0.84 77508_r_at RABEP2 1.05 6.58 0.45 0.77 1.04 6.47 0.57 0.89 1.04 6.52 0.34 0.65 1.04 6.50 0.59 0.91 209752_at REG1A 0.04 8.75 0.00 0.00 0.06 9.51 0.00 0.03 0.05 9.19 0.00 0.00 1.16 13.23 0.64 0.92 206286_s_at TDGF1 /// 1.46 6.26 0.03 0.20 1.19 6.32 0.11 0.51 1.30 6.30 0.01 0.08 0.92 4.88 0.49 0.88 TDGF3 205009_at TFF1 0.44 11.92 0.00 0.00 0.79 11.36 0.26 0.72 0.61 11.60 0.00 0.03 0.95 11.57 0.83 0.97 214476_at TFF2 0.37 7.00 0.00 0.01 0.80 6.72 0.26 0.71 0.58 6.84 0.00 0.03 1.31 7.02 0.34 0.81 204623_at TFF3 1.01 11.53 0.91 0.98 0.82 11.40 0.08 0.45 0.90 11.45 0.21 0.50 0.79 11.49 0.07 0.57 205016_at TGFA 1.20 7.35 0.25 0.60 1.40 7.57 0.00 0.10 1.31 7.48 0.01 0.05 1.19 7.62 0.04 0.52 211258_s_at TGFA 1.02 5.37 0.79 0.94 0.95 5.42 0.29 0.73 0.98 5.40 0.65 0.86 1.03 5.46 0.65 0.92 203085_s_at TGFB1 0.72 4.97 0.00 0.05 0.72 4.66 0.01 0.18 0.72 4.79 0.00 0.01 0.59 4.79 0.00 0.28 204858_s_at TYMP 0.47 6.64 0.00 0.00 0.64 6.60 0.00 0.07 0.56 6.62 0.00 0.00 0.92 7.06 0.42 0.85 210512_s_at VEGFA 0.81 9.21 0.22 0.57 1.07 9.06 0.63 0.91 0.95 9.12 0.66 0.86 1.11 9.52 0.10 0.63 210513_s_at VEGFA 0.79 6.53 0.05 0.26 1.10 6.34 0.40 0.81 0.96 6.42 0.64 0.85 1.03 6.64 0.72 0.94 211527_x_at VEGFA 0.71 6.15 0.02 0.16 1.01 5.83 0.95 0.99 0.87 5.97 0.20 0.49 1.03 6.23 0.78 0.96 212171_x_at VEGFA 0.82 7.26 0.11 0.40 1.07 7.04 0.44 0.84 0.96 7.13 0.59 0.83 1.06 7.28 0.36 0.82 209946_at VEGFC 0.85 4.51 0.15 0.47 0.85 4.33 0.00 0.10 0.85 4.40 0.01 0.04 0.89 4.42 0.34 0.81 205586_x_at VGF 0.88 5.31 0.07 0.31 1.02 5.30 0.74 0.95 0.96 5.30 0.42 0.71 1.16 5.32 0.03 0.46

Probe Set ID Gene Symbol UC NR after CDc NR after IBDc NR after CDi NR after therapy therapy (n=16) therapy (n=7) therapy (n=23) (n=10) vs vs vs vs UC NR before CDc NR before IBDc NR before CDi NR before therapy (n=16) therapy (n=7) therapy (n=23) therapy (n=10) FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR FC AveExpr p- FDR value value value value MMP 204475_at MMP1 0.26 9.97 0.04 0.32 0.55 11.82 0.04 1.00 0.33 10.54 0.02 0.22 0.57 10.96 0.00 0.21 genes 201069_at MMP2 0.59 8.14 0.10 0.45 0.68 9.19 0.26 1.00 0.62 8.46 0.06 0.35 0.73 8.12 0.04 0.57 205828_at MMP3 0.24 10.11 0.03 0.29 0.62 11.69 0.07 1.00 0.32 10.59 0.02 0.21 0.25 9.39 0.00 0.06 204259_at MMP7 0.47 8.23 0.02 0.28 0.81 8.04 0.36 1.00 0.55 8.17 0.02 0.23 0.56 6.56 0.01 0.39 203936_s_at MMP9 0.35 7.68 0.00 0.16 0.56 8.58 0.07 1.00 0.40 7.96 0.00 0.08 0.45 6.67 0.00 0.07 205680_at MMP10 0.27 7.07 0.01 0.20 0.56 7.40 0.06 1.00 0.34 7.17 0.00 0.12 0.41 5.36 0.00 0.24 204580_at MMP12 0.43 10.79 0.02 0.25 0.91 11.32 0.75 1.00 0.54 10.95 0.02 0.25 0.40 9.16 0.00 0.12 160020_at MMP14 0.82 6.40 0.00 0.16 0.93 6.43 0.49 1.00 0.85 6.41 0.01 0.15 1.03 6.30 0.68 0.95 202827_s_at MMP14 0.72 6.00 0.00 0.10 0.84 6.16 0.08 1.00 0.76 6.05 0.00 0.06 0.99 5.70 0.88 0.98 202828_s_at MMP14 0.81 6.47 0.00 0.16 0.89 6.61 0.14 1.00 0.84 6.51 0.00 0.09 0.89 6.35 0.11 0.70 203365_s_at MMP15 1.15 6.68 0.15 0.53 1.14 6.60 0.27 1.00 1.14 6.66 0.08 0.40 1.35 7.19 0.02 0.48 204574_s_at MMP19 0.98 5.51 0.68 0.90 1.00 5.49 0.95 1.00 0.98 5.51 0.70 0.90 1.02 5.61 0.77 0.97 204575_s_at MMP19 0.77 5.87 0.20 0.58 0.90 6.45 0.68 1.00 0.81 6.04 0.20 0.58 0.79 5.33 0.04 0.56 227106_at MMP19 0.98 5.47 0.63 0.87 1.12 5.55 0.14 1.00 1.02 5.49 0.60 0.86 1.03 5.69 0.63 0.94 221953_s_at MMP24 /// 1.09 6.93 0.22 0.61 1.00 6.91 0.96 1.00 1.06 6.93 0.28 0.66 1.08 7.15 0.18 0.76 LOC729580 49679_s_at MMP24 /// 1.00 6.73 1.00 1.00 1.05 6.70 0.41 1.00 1.02 6.72 0.63 0.88 1.04 6.87 0.66 0.94 LOC729580 207890_s_at MMP25 0.86 5.76 0.00 0.16 1.03 5.87 0.75 1.00 0.91 5.79 0.04 0.31 0.97 5.81 0.77 0.97 219909_at MMP28 1.31 5.07 0.07 0.40 1.02 5.14 0.93 1.00 1.21 5.09 0.11 0.46 1.14 5.11 0.47 0.89 222937_s_at MMP28 1.06 5.96 0.46 0.79 0.93 5.85 0.55 1.00 1.02 5.93 0.81 0.95 1.14 5.98 0.15 0.73 224207_x_at MMP28 1.04 6.76 0.57 0.85 1.06 6.71 0.48 1.00 1.05 6.74 0.40 0.75 1.12 6.91 0.11 0.71 239272_at MMP28 1.14 6.14 0.37 0.74 0.87 6.17 0.50 1.00 1.05 6.15 0.69 0.90 1.00 6.25 0.97 1.00 239273_s_at MMP28 1.03 6.24 0.82 0.94 0.97 6.35 0.86 1.00 1.01 6.28 0.92 0.98 1.00 6.26 0.97 1.00 TIMP 201666_at TIMP1 0.57 10.59 0.01 0.23 0.72 10.96 0.10 1.00 0.61 10.70 0.00 0.14 0.70 9.77 0.01 0.36 genes 203167_at TIMP2 0.68 6.58 0.02 0.25 0.78 6.76 0.09 1.00 0.71 6.64 0.01 0.14 1.11 6.94 0.44 0.88 224560_at TIMP2 0.66 7.86 0.08 0.41 0.84 8.42 0.45 1.00 0.71 8.03 0.06 0.36 0.95 7.88 0.70 0.95 231579_s_at TIMP2 0.68 9.07 0.13 0.50 0.82 9.59 0.34 1.00 0.72 9.23 0.09 0.42 0.92 9.12 0.52 0.91 201147_s_at TIMP3 0.92 5.10 0.64 0.88 0.89 5.41 0.70 1.00 0.91 5.19 0.56 0.84 1.06 4.68 0.63 0.94 201148_s_at TIMP3 0.91 6.46 0.09 0.44 0.92 6.49 0.47 1.00 0.91 6.47 0.09 0.42 0.96 6.31 0.57 0.92 201149_s_at TIMP3 0.88 5.32 0.22 0.61 0.94 5.82 0.81 1.00 0.90 5.47 0.35 0.72 0.98 4.96 0.86 0.98 201150_s_at TIMP3 0.87 6.39 0.38 0.75 0.87 6.66 0.62 1.00 0.87 6.47 0.34 0.71 0.91 5.66 0.56 0.92 ADAM 205180_s_at ADAM8 0.82 5.87 0.09 0.44 0.98 6.18 0.91 1.00 0.87 5.96 0.13 0.49 0.90 5.90 0.13 0.72 genes 1555326_a_at ADAM9 0.82 7.79 0.05 0.36 0.74 7.43 0.21 1.00 0.80 7.68 0.03 0.28 0.70 6.66 0.08 0.66 202381_at ADAM9 0.97 10.10 0.68 0.90 0.79 9.89 0.09 1.00 0.91 10.03 0.18 0.56 0.84 9.53 0.28 0.81 202604_x_at ADAM10 0.92 6.64 0.24 0.63 0.93 6.54 0.44 1.00 0.92 6.61 0.16 0.54 0.83 6.17 0.13 0.72 214895_s_at ADAM10 0.96 6.62 0.55 0.84 0.85 6.60 0.17 1.00 0.93 6.62 0.19 0.57 0.77 6.06 0.16 0.74 1555896_a_at ADAM15 0.96 6.88 0.25 0.64 0.95 6.84 0.52 1.00 0.95 6.87 0.19 0.57 0.95 6.64 0.45 0.89 217007_s_at ADAM15 1.04 5.88 0.55 0.84 0.99 5.82 0.95 1.00 1.02 5.86 0.69 0.90 1.02 5.56 0.75 0.96 205745_x_at ADAM17 1.05 6.23 0.46 0.79 1.03 6.28 0.78 1.00 1.05 6.24 0.45 0.78 1.04 6.05 0.49 0.90 209765_at ADAM19 0.64 6.23 0.00 0.17 1.08 6.53 0.68 1.00 0.75 6.32 0.03 0.27 0.75 5.82 0.02 0.51 205997_at ADAM28 0.53 5.98 0.00 0.11 0.82 6.28 0.24 1.00 0.61 6.07 0.00 0.08 0.65 6.31 0.00 0.29 208269_s_at ADAM28 0.93 5.36 0.19 0.57 0.96 5.28 0.61 1.00 0.94 5.33 0.16 0.53 1.00 5.35 0.96 0.99 233868_x_at ADAM33 1.17 6.86 0.02 0.28 1.12 6.80 0.23 1.00 1.16 6.84 0.01 0.19 1.06 6.88 0.37 0.86 206134_at ADAMDEC1 0.80 8.09 0.11 0.46 0.78 8.39 0.05 1.00 0.79 8.18 0.03 0.27 0.80 8.64 0.22 0.79 222162_s_at ADAMTS1 0.97 6.24 0.90 0.97 0.97 6.67 0.94 1.00 0.97 6.37 0.89 0.97 0.79 5.40 0.11 0.70 235368_at ADAMTS5 0.79 5.47 0.07 0.40 0.91 5.75 0.70 1.00 0.82 5.55 0.11 0.46 1.23 6.27 0.11 0.70 220705_s_at ADAMTS7 1.05 5.41 0.25 0.64 1.01 5.41 0.93 1.00 1.04 5.41 0.37 0.73 1.08 5.62 0.33 0.84 226814_at ADAMTS9 0.81 6.76 0.16 0.54 0.89 6.71 0.45 1.00 0.83 6.75 0.12 0.47 0.91 5.77 0.54 0.91 220208_at ADAMTS13 1.04 5.68 0.41 0.77 0.97 5.71 0.72 1.00 1.02 5.69 0.62 0.87 1.03 5.59 0.57 0.92 Growth 212285_s_at AGRN 0.95 6.86 0.48 0.80 0.95 6.68 0.58 1.00 0.95 6.80 0.37 0.73 1.06 6.57 0.52 0.91 factor genes 217410_at AGRN 1.11 5.48 0.08 0.42 0.99 5.37 0.89 1.00 1.07 5.45 0.14 0.50 1.05 5.48 0.45 0.89 217419_x_at AGRN 0.91 6.52 0.16 0.55 0.94 6.33 0.56 1.00 0.92 6.46 0.14 0.51 1.02 6.31 0.79 0.97 202834_at AGT 0.68 6.01 0.00 0.14 0.69 5.70 0.06 1.00 0.69 5.91 0.00 0.07 0.80 5.58 0.06 0.63 213001_at ANGPTL2 0.62 6.71 0.07 0.39 0.74 7.38 0.36 1.00 0.65 6.91 0.05 0.33 0.79 6.40 0.00 0.28 213004_at ANGPTL2 0.71 5.15 0.09 0.44 0.70 5.53 0.15 1.00 0.71 5.27 0.04 0.30 0.85 4.86 0.13 0.71 221009_s_at ANGPTL4 0.65 6.21 0.00 0.07 0.64 5.87 0.02 1.00 0.65 6.11 0.00 0.03 1.20 6.30 0.07 0.64 223333_s_at ANGPTL4 0.70 5.36 0.00 0.10 0.74 5.24 0.03 1.00 0.71 5.33 0.00 0.04 1.06 5.44 0.51 0.91 205239_at AREG 1.14 9.03 0.45 0.78 1.65 8.50 0.02 1.00 1.28 8.87 0.09 0.42 0.88 6.41 0.54 0.91 210237_at ARTN 1.07 5.61 0.43 0.77 1.03 5.57 0.75 1.00 1.06 5.60 0.40 0.75 0.98 5.37 0.76 0.96 202701_at BMP1 1.00 6.02 0.99 1.00 0.93 6.16 0.38 1.00 0.98 6.06 0.63 0.87 1.09 6.03 0.32 0.84 205574_x_at BMP1 0.74 5.50 0.01 0.21 0.97 5.75 0.84 1.00 0.80 5.57 0.02 0.24 1.18 5.43 0.11 0.70 206725_x_at BMP1 0.89 5.31 0.05 0.36 1.14 5.46 0.13 1.00 0.96 5.35 0.40 0.75 1.10 5.42 0.32 0.84 207595_s_at BMP1 0.83 5.59 0.01 0.20 0.92 5.82 0.41 1.00 0.85 5.66 0.01 0.17 1.08 5.52 0.38 0.86 205289_at BMP2 1.04 8.90 0.67 0.89 0.96 8.74 0.68 1.00 1.02 8.85 0.82 0.95 0.95 7.59 0.71 0.96 205290_s_at BMP2 0.94 8.19 0.54 0.84 1.03 7.92 0.73 1.00 0.96 8.11 0.64 0.88 1.16 7.12 0.10 0.68 211518_s_at BMP4 0.91 5.47 0.12 0.48 0.94 5.47 0.64 1.00 0.92 5.47 0.15 0.52 0.97 5.37 0.66 0.94 211260_at BMP7 1.07 5.77 0.07 0.40 1.03 5.77 0.61 1.00 1.06 5.77 0.06 0.36 1.02 5.83 0.70 0.95 220203_at BMP8A 0.89 5.47 0.01 0.21 0.85 5.62 0.07 1.00 0.88 5.52 0.00 0.10 1.04 5.51 0.58 0.92 218529_at CD320 1.00 7.12 0.95 0.98 0.93 7.00 0.45 1.00 0.98 7.09 0.70 0.91 0.98 6.52 0.78 0.97 219505_at CECR1 0.61 7.38 0.01 0.21 0.93 7.59 0.67 1.00 0.69 7.44 0.01 0.20 0.76 6.47 0.00 0.22 219500_at CLCF1 0.96 5.65 0.42 0.77 0.98 5.53 0.84 1.00 0.96 5.62 0.46 0.79 0.98 5.32 0.70 0.95 207442_at CSF3 0.73 6.19 0.03 0.29 0.81 6.49 0.31 1.00 0.76 6.28 0.02 0.23 0.91 6.06 0.40 0.87 209101_at CTGF 0.82 7.92 0.36 0.73 1.24 8.04 0.37 1.00 0.93 7.96 0.69 0.90 0.76 6.46 0.08 0.66 205767_at EREG 0.91 7.27 0.70 0.90 1.74 7.13 0.05 1.00 1.11 7.23 0.58 0.86 0.72 5.17 0.12 0.71 218255_s_at FBRS 1.08 6.10 0.25 0.64 1.02 6.12 0.78 1.00 1.06 6.11 0.24 0.62 1.07 6.25 0.33 0.84 204421_s_at FGF2 0.80 5.27 0.06 0.37 0.77 5.49 0.03 1.00 0.79 5.34 0.01 0.17 0.90 4.86 0.23 0.79 208417_at FGF6 0.96 5.50 0.30 0.68 1.06 5.53 0.56 1.00 0.99 5.51 0.75 0.93 1.04 5.59 0.54 0.91 1554741_s_at FGF7 /// 0.68 5.36 0.22 0.61 0.76 5.91 0.39 1.00 0.71 5.53 0.16 0.53 0.86 4.64 0.20 0.77 KGFLP1 /// KGFLP2 206404_at FGF9 1.25 4.53 0.02 0.24 1.39 4.72 0.04 1.00 1.29 4.59 0.00 0.11 1.26 5.96 0.00 0.27 221136_at GDF2 1.04 5.90 0.38 0.74 1.08 5.81 0.29 1.00 1.05 5.87 0.18 0.56 1.02 5.91 0.75 0.96 206614_at GDF5 1.04 5.75 0.42 0.77 1.03 5.70 0.58 1.00 1.04 5.74 0.31 0.69 1.05 5.79 0.41 0.87 221577_x_at GDF15/// 1.27 6.86 0.19 0.58 1.18 6.56 0.27 1.00 1.24 6.77 0.12 0.47 0.81 5.46 0.05 0.61 LOC100287132 /// LOC100292463 202543_s_at GMFB 1.00 8.31 0.95 0.99 0.95 8.24 0.66 1.00 0.99 8.29 0.82 0.95 0.88 7.77 0.24 0.80 202544_at GMFB 1.11 8.74 0.02 0.26 1.05 8.71 0.45 1.00 1.09 8.73 0.01 0.21 0.99 8.77 0.87 0.98 204220_at GMFG 0.71 7.20 0.10 0.45 1.01 7.72 0.97 1.00 0.79 7.36 0.17 0.54 0.75 6.84 0.00 0.33 208308_s_at GPI 0.99 9.76 0.82 0.95 0.88 9.67 0.24 1.00 0.96 9.73 0.32 0.70 0.96 9.39 0.68 0.95 200678_x_at GRN 0.99 9.02 0.81 0.94 0.95 9.20 0.39 1.00 0.98 9.07 0.53 0.83 0.88 8.89 0.17 0.75 211284_s_at GRN 1.03 8.39 0.56 0.84 0.99 8.54 0.90 1.00 1.02 8.44 0.63 0.88 0.91 8.25 0.37 0.86 216041_x_at GRN 1.00 9.01 0.94 0.98 0.97 9.17 0.63 1.00 0.99 9.06 0.76 0.93 0.91 8.83 0.30 0.83 203821_at HBEGF 1.23 8.12 0.38 0.75 2.02 7.43 0.01 1.00 1.43 7.91 0.07 0.38 1.02 6.38 0.89 0.99 38037_at HBEGF 1.28 7.82 0.31 0.69 2.03 7.24 0.01 1.00 1.47 7.64 0.04 0.32 1.05 6.39 0.69 0.95 200896_x_at HDGF 1.02 9.36 0.63 0.87 1.07 9.27 0.26 1.00 1.03 9.33 0.27 0.65 1.09 9.60 0.21 0.78 216484_x_at HDGF 1.03 8.58 0.45 0.79 0.99 8.45 0.85 1.00 1.02 8.54 0.57 0.85 1.07 8.80 0.24 0.80 209524_at HDGFRP3 0.84 5.99 0.32 0.70 0.79 6.23 0.26 1.00 0.82 6.06 0.17 0.55 0.81 5.05 0.06 0.63 209526_s_at HDGFRP3 0.88 5.61 0.27 0.66 0.79 5.83 0.17 1.00 0.85 5.68 0.10 0.45 0.85 4.86 0.13 0.72 216693_x_at HDGFRP3 0.84 5.76 0.16 0.54 0.79 6.08 0.20 1.00 0.83 5.86 0.07 0.38 0.92 5.00 0.32 0.83 211577_s_at IGF1 0.96 5.59 0.43 0.78 1.03 5.68 0.58 1.00 0.98 5.61 0.64 0.88 0.84 5.53 0.01 0.39 202409_at IGF2 /// INS- 0.95 5.25 0.65 0.89 0.99 5.65 0.95 1.00 0.96 5.37 0.72 0.91 1.01 5.22 0.93 0.99 IGF2 210511_s_at INHBA 0.45 5.92 0.03 0.30 1.08 7.12 0.77 1.00 0.59 6.29 0.06 0.36 0.57 5.61 0.00 0.24 209098_s_at JAG1 0.89 6.77 0.14 0.52 0.98 6.52 0.88 1.00 0.91 6.69 0.23 0.62 0.82 5.62 0.11 0.70 209099_x_at JAG1 0.99 10.35 0.83 0.95 1.03 10.22 0.79 1.00 1.00 10.31 0.98 1.00 0.93 9.68 0.47 0.90 216268_s_at JAG1 0.99 10.37 0.90 0.97 1.03 10.24 0.78 1.00 1.00 10.33 0.93 0.98 0.92 9.62 0.50 0.90 231183_s_at JAG1 0.94 6.03 0.46 0.79 1.00 5.88 0.97 1.00 0.96 5.98 0.56 0.84 0.91 5.36 0.45 0.89 209784_s_at JAG2 1.04 5.36 0.54 0.83 1.06 5.41 0.62 1.00 1.04 5.38 0.44 0.77 1.18 5.66 0.06 0.63 32137_at JAG2 1.03 5.76 0.64 0.88 0.95 5.87 0.72 1.00 1.01 5.79 0.93 0.98 1.17 6.23 0.09 0.68 226534_at KITLG 1.29 7.73 0.01 0.19 0.91 7.93 0.30 1.00 1.16 7.79 0.04 0.32 0.87 7.62 0.14 0.72 206268_at LEFTY1 1.57 8.90 0.02 0.27 0.93 8.96 0.54 1.00 1.33 8.91 0.05 0.34 0.56 5.18 0.14 0.72 205266_at LIF 0.87 6.28 0.10 0.46 1.17 5.90 0.29 1.00 0.95 6.17 0.51 0.82 1.13 5.68 0.20 0.77 1559361_at MACC1 0.86 4.35 0.07 0.40 0.89 4.15 0.21 1.00 0.87 4.29 0.03 0.28 1.12 5.19 0.50 0.90 1566764_at MACC1 0.92 4.06 0.39 0.75 1.00 3.77 0.98 1.00 0.94 3.97 0.52 0.82 1.09 5.27 0.65 0.94 1566766_a_at MACC1 0.98 5.36 0.69 0.90 1.03 5.14 0.81 1.00 1.00 5.29 0.95 0.99 1.05 6.26 0.47 0.89 232151_at MACC1 1.04 5.15 0.53 0.83 1.00 4.94 0.98 1.00 1.03 5.08 0.58 0.86 1.04 6.19 0.65 0.94 202655_at MANF 0.93 9.36 0.27 0.65 1.05 9.31 0.44 1.00 0.97 9.35 0.46 0.79 0.99 8.75 0.88 0.98 209035_at MDK 0.91 7.72 0.39 0.75 0.98 8.03 0.91 1.00 0.93 7.82 0.47 0.79 1.02 8.62 0.88 0.98 206560_s_at MIA 0.87 6.03 0.09 0.43 1.14 6.26 0.15 1.00 0.95 6.10 0.39 0.75 0.69 5.97 0.01 0.38 205614_x_at MST1 0.97 6.18 0.60 0.86 1.06 5.92 0.48 1.00 0.99 6.10 0.91 0.98 1.37 7.48 0.00 0.24 216320_x_at MST1 0.99 6.20 0.85 0.96 1.12 5.91 0.14 1.00 1.03 6.11 0.56 0.84 1.35 7.69 0.01 0.36 214075_at NENF 1.06 5.98 0.30 0.69 1.04 5.98 0.65 1.00 1.05 5.98 0.26 0.64 1.06 5.81 0.47 0.89 218407_x_at NENF 1.03 7.88 0.60 0.86 1.07 7.87 0.29 1.00 1.04 7.88 0.33 0.70 0.91 7.80 0.16 0.74 208232_x_at NRG1 1.05 5.21 0.45 0.79 1.03 5.14 0.65 1.00 1.04 5.19 0.37 0.73 1.09 5.17 0.15 0.73 230329_s_at NUDT6 1.25 6.11 0.00 0.15 1.01 6.17 0.93 1.00 1.17 6.13 0.01 0.18 0.81 5.59 0.09 0.68 219475_at OSGIN1 1.00 5.32 0.95 0.99 0.96 5.39 0.67 1.00 0.99 5.34 0.78 0.94 1.23 5.95 0.01 0.44 214637_at OSM 0.85 5.36 0.19 0.58 1.24 5.78 0.18 1.00 0.95 5.49 0.64 0.88 0.88 5.38 0.36 0.85 230170_at OSM 0.68 5.34 0.10 0.46 1.38 6.22 0.12 1.00 0.85 5.61 0.37 0.73 0.79 5.30 0.28 0.82 205463_s_at PDGFA 1.10 6.98 0.36 0.73 0.97 7.04 0.66 1.00 1.05 6.99 0.48 0.80 1.14 7.23 0.07 0.64 216867_s_at PDGFA 0.97 5.01 0.70 0.91 0.98 5.07 0.85 1.00 0.97 5.03 0.68 0.90 1.22 5.45 0.07 0.64 229830_at PDGFA 1.23 7.76 0.08 0.41 0.95 7.83 0.40 1.00 1.14 7.78 0.13 0.50 1.08 8.09 0.54 0.91 216061_x_at PDGFB 0.92 5.55 0.08 0.42 0.95 5.51 0.40 1.00 0.93 5.54 0.04 0.32 1.02 5.53 0.82 0.98 218718_at PDGFC 0.76 5.51 0.03 0.29 1.13 5.74 0.56 1.00 0.85 5.58 0.17 0.55 0.91 6.42 0.32 0.84 225064_at RABEP1 0.96 6.48 0.49 0.81 0.89 6.54 0.10 1.00 0.94 6.50 0.15 0.51 0.84 6.30 0.11 0.70 225092_at RABEP1 1.03 6.96 0.66 0.89 1.00 6.87 1.00 1.00 1.02 6.93 0.69 0.90 0.98 6.92 0.79 0.97 219057_at RABEP2 1.06 5.50 0.33 0.71 1.05 5.47 0.54 1.00 1.06 5.49 0.24 0.62 1.02 5.71 0.78 0.97 74694_s_at RABEP2 1.02 6.37 0.70 0.90 0.96 6.43 0.57 1.00 1.00 6.39 0.97 0.99 1.00 6.58 0.97 1.00 77508_r_at RABEP2 1.00 6.35 0.95 0.99 0.99 6.35 0.93 1.00 1.00 6.35 0.92 0.98 1.08 6.51 0.22 0.79 209752_at REG1A 0.32 10.44 0.00 0.15 0.83 11.88 0.64 1.00 0.42 10.88 0.01 0.15 0.87 13.34 0.28 0.82 206286_s_at TDGF1 /// 1.35 6.00 0.03 0.30 1.17 5.70 0.05 1.00 1.29 5.91 0.01 0.18 0.86 4.87 0.11 0.71 TDGF3 205009_at TFF1 0.78 12.19 0.01 0.23 0.71 11.90 0.12 1.00 0.76 12.10 0.01 0.16 0.83 12.30 0.14 0.73 214476_at TFF2 0.61 7.34 0.01 0.21 0.72 7.39 0.29 1.00 0.64 7.35 0.01 0.17 0.66 8.70 0.11 0.70 204623_at TFF3 1.05 11.20 0.68 0.90 0.93 11.28 0.62 1.00 1.01 11.23 0.93 0.98 0.86 11.54 0.08 0.66 205016_at TGFA 0.90 7.27 0.31 0.69 0.91 7.44 0.56 1.00 0.91 7.32 0.25 0.63 0.99 7.47 0.94 0.99 211258_s_at TGFA 0.88 5.30 0.05 0.34 1.07 5.38 0.42 1.00 0.93 5.33 0.19 0.58 1.07 5.36 0.48 0.90 203085_s_at TGFB1 0.65 5.81 0.04 0.32 0.89 6.34 0.52 1.00 0.72 5.97 0.03 0.29 0.83 5.68 0.20 0.77 204858_s_at TYMP 0.74 7.23 0.02 0.27 0.92 7.52 0.51 1.00 0.79 7.32 0.02 0.24 0.98 7.44 0.84 0.98 210512_s_at VEGFA 0.98 9.37 0.90 0.97 0.92 9.02 0.43 1.00 0.96 9.27 0.68 0.90 1.12 9.31 0.33 0.84 210513_s_at VEGFA 0.89 6.61 0.12 0.49 0.81 6.26 0.23 1.00 0.87 6.50 0.06 0.37 1.02 6.42 0.81 0.97 211527_x_at VEGFA 0.83 6.21 0.10 0.46 0.90 5.87 0.46 1.00 0.85 6.11 0.08 0.41 1.03 5.94 0.82 0.97 212171_x_at VEGFA 0.93 7.29 0.27 0.66 0.94 7.04 0.37 1.00 0.93 7.22 0.17 0.54 0.92 7.10 0.39 0.87 209946_at VEGFC 0.93 5.01 0.61 0.87 1.06 5.54 0.82 1.00 0.97 5.17 0.81 0.95 0.85 5.04 0.20 0.77 205586_x_at VGF 1.00 5.34 0.97 0.99 1.04 5.14 0.61 1.00 1.01 5.28 0.71 0.91 0.99 5.36 0.89 0.99

Probe Set ID Gene Symbol Probe Set ID annotated by

MMP genes 204475_at MMP1 Affymetrix NetAffx website 201069_at MMP2 Affymetrix NetAffx website 205828_at MMP3 Affymetrix NetAffx website 204259_at MMP7 Affymetrix NetAffx website 203936_s_at MMP9 Affymetrix NetAffx website 205680_at MMP10 Affymetrix NetAffx website 204580_at MMP12 Affymetrix NetAffx website 160020_at MMP14 Affymetrix NetAffx website 202827_s_at MMP14 Affymetrix NetAffx website 202828_s_at MMP14 Affymetrix NetAffx website 203365_s_at MMP15 Affymetrix NetAffx website 204574_s_at MMP19 Affymetrix NetAffx website 204575_s_at MMP19 Affymetrix NetAffx website 227106_at MMP19 UCSC Genome Browser website and/or NCBI website 221953_s_at MMP24 /// LOC729580 UCSC Genome Browser website and/or NCBI website 49679_s_at MMP24 /// LOC729580 UCSC Genome Browser website and/or NCBI website 207890_s_at MMP25 Affymetrix NetAffx website 219909_at MMP28 Affymetrix NetAffx website 222937_s_at MMP28 Affymetrix NetAffx website 224207_x_at MMP28 Affymetrix NetAffx website 239272_at MMP28 Affymetrix NetAffx website 239273_s_at MMP28 Affymetrix NetAffx website TIMP genes 201666_at TIMP1 Affymetrix NetAffx website 203167_at TIMP2 Affymetrix NetAffx website 224560_at TIMP2 Affymetrix NetAffx website 231579_s_at TIMP2 Affymetrix NetAffx website 201147_s_at TIMP3 Affymetrix NetAffx website 201148_s_at TIMP3 Affymetrix NetAffx website 201149_s_at TIMP3 Affymetrix NetAffx website 201150_s_at TIMP3 Affymetrix NetAffx website ADAM genes 205180_s_at ADAM8 Affymetrix NetAffx website 1555326_a_a ADAM9 Affymetrix NetAffx website t 202381_at ADAM9 Affymetrix NetAffx website 202604_x_at ADAM10 Affymetrix NetAffx website 214895_s_at ADAM10 Affymetrix NetAffx website 1555896_a_a ADAM15 Affymetrix NetAffx website t 217007_s_at ADAM15 Affymetrix NetAffx website 205745_x_at ADAM17 Affymetrix NetAffx website 209765_at ADAM19 Affymetrix NetAffx website 205997_at ADAM28 Affymetrix NetAffx website 208269_s_at ADAM28 Affymetrix NetAffx website 233868_x_at ADAM33 Affymetrix NetAffx website 206134_at ADAMDEC1 Affymetrix NetAffx website 222162_s_at ADAMTS1 Affymetrix NetAffx website 235368_at ADAMTS5 Affymetrix NetAffx website 220705_s_at ADAMTS7 Affymetrix NetAffx website 226814_at ADAMTS9 Affymetrix NetAffx website 220208_at ADAMTS13 Affymetrix NetAffx website Growth factor genes 212285_s_at AGRN Affymetrix NetAffx website 217410_at AGRN Affymetrix NetAffx website 217419_x_at AGRN Affymetrix NetAffx website 202834_at AGT Affymetrix NetAffx website 213001_at ANGPTL2 Affymetrix NetAffx website 213004_at ANGPTL2 Affymetrix NetAffx website 221009_s_at ANGPTL4 Affymetrix NetAffx website 223333_s_at ANGPTL4 Affymetrix NetAffx website 205239_at AREG Affymetrix NetAffx website 210237_at ARTN Affymetrix NetAffx website 202701_at BMP1 Affymetrix NetAffx website 205574_x_at BMP1 Affymetrix NetAffx website 206725_x_at BMP1 Affymetrix NetAffx website 207595_s_at BMP1 Affymetrix NetAffx website 205289_at BMP2 Affymetrix NetAffx website 205290_s_at BMP2 Affymetrix NetAffx website 211518_s_at BMP4 Affymetrix NetAffx website 211260_at BMP7 Affymetrix NetAffx website 220203_at BMP8A Affymetrix NetAffx website 218529_at CD320 Affymetrix NetAffx website 219505_at CECR1 Affymetrix NetAffx website 219500_at CLCF1 Affymetrix NetAffx website 207442_at CSF3 Affymetrix NetAffx website 209101_at CTGF Affymetrix NetAffx website 205767_at EREG Affymetrix NetAffx website 218255_s_at FBRS Affymetrix NetAffx website 204421_s_at FGF2 Affymetrix NetAffx website 208417_at FGF6 Affymetrix NetAffx website 1554741_s_at FGF7 /// KGFLP1 /// Affymetrix NetAffx website KGFLP2 206404_at FGF9 Affymetrix NetAffx website 221136_at GDF2 Affymetrix NetAffx website 206614_at GDF5 Affymetrix NetAffx website 221577_x_at GDF15/// UCSC Genome Browser website and/or NCBI website LOC100287132 /// LOC100292463 202543_s_at GMFB Affymetrix NetAffx website 202544_at GMFB Affymetrix NetAffx website 204220_at GMFG Affymetrix NetAffx website 208308_s_at GPI Affymetrix NetAffx website 200678_x_at GRN Affymetrix NetAffx website 211284_s_at GRN Affymetrix NetAffx website 216041_x_at GRN Affymetrix NetAffx website 203821_at HBEGF Affymetrix NetAffx website 38037_at HBEGF Affymetrix NetAffx website 200896_x_at HDGF Affymetrix NetAffx website 216484_x_at HDGF Affymetrix NetAffx website 209524_at HDGFRP3 Affymetrix NetAffx website 209526_s_at HDGFRP3 Affymetrix NetAffx website 216693_x_at HDGFRP3 Affymetrix NetAffx website 211577_s_at IGF1 Affymetrix NetAffx website 202409_at IGF2 /// INS-IGF2 Affymetrix NetAffx website 210511_s_at INHBA Affymetrix NetAffx website 209098_s_at JAG1 Affymetrix NetAffx website 209099_x_at JAG1 Affymetrix NetAffx website 216268_s_at JAG1 Affymetrix NetAffx website 231183_s_at JAG1 Affymetrix NetAffx website 209784_s_at JAG2 Affymetrix NetAffx website 32137_at JAG2 Affymetrix NetAffx website 226534_at KITLG Affymetrix NetAffx website 206268_at LEFTY1 Affymetrix NetAffx website 205266_at LIF Affymetrix NetAffx website 1559361_at MACC1 Affymetrix NetAffx website 1566764_at MACC1 Affymetrix NetAffx website 1566766_a_a MACC1 Affymetrix NetAffx website t 232151_at MACC1 Affymetrix NetAffx website 202655_at MANF Affymetrix NetAffx website 209035_at MDK Affymetrix NetAffx website 206560_s_at MIA Affymetrix NetAffx website 205614_x_at MST1 Affymetrix NetAffx website 216320_x_at MST1 Affymetrix NetAffx website 214075_at NENF Affymetrix NetAffx website 218407_x_at NENF Affymetrix NetAffx website 208232_x_at NRG1 Affymetrix NetAffx website 230329_s_at NUDT6 Affymetrix NetAffx website 219475_at OSGIN1 Affymetrix NetAffx website 214637_at OSM Affymetrix NetAffx website 230170_at OSM Affymetrix NetAffx website 205463_s_at PDGFA Affymetrix NetAffx website 216867_s_at PDGFA Affymetrix NetAffx website 229830_at PDGFA UCSC Genome Browser website and/or NCBI website 216061_x_at PDGFB Affymetrix NetAffx website 218718_at PDGFC Affymetrix NetAffx website 225064_at RABEP1 Affymetrix NetAffx website 225092_at RABEP1 Affymetrix NetAffx website 219057_at RABEP2 Affymetrix NetAffx website 74694_s_at RABEP2 Affymetrix NetAffx website 77508_r_at RABEP2 Affymetrix NetAffx website 209752_at REG1A Affymetrix NetAffx website 206286_s_at TDGF1 /// TDGF3 Affymetrix NetAffx website 205009_at TFF1 Affymetrix NetAffx website 214476_at TFF2 Affymetrix NetAffx website 204623_at TFF3 Affymetrix NetAffx website 205016_at TGFA Affymetrix NetAffx website 211258_s_at TGFA Affymetrix NetAffx website 203085_s_at TGFB1 Affymetrix NetAffx website 204858_s_at TYMP Affymetrix NetAffx website 210512_s_at VEGFA Affymetrix NetAffx website 210513_s_at VEGFA Affymetrix NetAffx website 211527_x_at VEGFA Affymetrix NetAffx website 212171_x_at VEGFA Affymetrix NetAffx website 209946_at VEGFC Affymetrix NetAffx website 205586_x_at VGF Affymetrix NetAffx website