A Gene Original study GSE12251 COLON BIOPSY GSE16879 COLON BIOPSY GSE23597 COLON BIOPSY GSE42296 PBMC Symbol Full name Disease n Ref AUC p-value AUC p-value AUC p-value AUC p-value WNT5A wingless-type MMTV integration site family, member 5A CU 46 [24] 0.95* 1.00E-10* 0.92 4.70E-13 0.77 8.1E-03 0.59 0.17 CSF3 colony stimulating factor 3 IBD 16 [27] 0.89 8.30E-10 0.84 1.30E-05 0.81 2.77 E-03 0.58 0.19 PTGS2 prostaglandin-endoperoxide synthase 2 IBD 16 [27] 0.97 <1E-16 0.87 5.20E-07 0.83 1.11 E-04 0.61 0.12 TNF tumor necrosis factor IBD 16 [27] 0.78 2.70E-03 0.72 0.02 0.82 3.37 E-04 0.63 0.08 G0S2 G0/G1switch 2 CD 37 [28] 0.99 <1E-16 0.85 8.71E-05 0.80 1.97 E-04 0.59 0.17 S100A8 S100 calcium binding protein A8 CD 37 [28] 0.89 1.30E-09 0.84 7.60E-05 0.85 1.58 E-06 0.66 0.03 IL6 interleukin 6 IBD 16 [27] 0.92 1.49E-11 0.87 5.35E-07 0.81 1.62 E-04 0.57 0.22 IL8 interleukin 8 IBD 16 [27] 0.95 <1E-16 0.8 8.51E-04 0.75 4.80 E-03 0.51 0.45 CXCL6 chemokine (C-X-C motif) ligand 6 CU 46 [24] 0.73* 0.018* 0.88 4.10E-07 0.70 0.044 0.62 0.10 SELP selectin P IBD 16 [27] 0.9 2.70E-10 0.68 0.077 0.85 1.83 E-05 0.73 0.003 ACSL4 acyl-CoA synthetase long-chain family member 4 CU 46 [24] 0.75* 0.041* 0.89 5.60E-09 0.84 1.30E-05 0.64 0.06 CD80 CD80 molecule IBD 16 [27] 0.68 0.06 0.78 0.0020 0.69 0.07 0.61 0.13 CD86 CD86 molecule IBD 16 [27] 0.76 0.024 0.75 0.012 0.87 7.80E-07 0.78 2.40E-04 CXCL10 chemokine (C-X-C motif) ligand 10 IBD 16 [27] 0.68 0.08 0.71 0.03 0.8 0.0004 0.58 0.21 CSF2 colony stimulating factor 2 (granulocyte-macrophage) IBD 16 [27] 0.69 0.1 0.8 0.001 0.79 0.0007 0.54 0.32 IGFBP5 insulin-like growth factor binding protein 5 CU 46 [24] 0.72* 0.07* 0.77 0.005 0.91 2.91E-13 0.57 0.22 IL10 interleukin 10 CU 37 [28] 0.72 0.038 0.74 0.011 0.87 4.20E-06 0.61 0.12 IL13RA2 interleukin 13 receptor, alpha 2 CU 46 [24] 0.78* 0.043* 0.9 1.30E-09 0.95 <1E-16 0.64 0.058 IL1A interleukin 1, alpha IBD 16 [27] 0.73 0.07 0.94 <1E-16 0.77 0.003869 0.62 0.09 IL1B interleukin 1, beta IBD 16 [27] 0.72 0.15 0.97 <1E-16 0.81 0.0003 0.5 0.5 LPHN2 latrophilin 2 CU 46 [24] 0.72* 0.06* 0.78 0.006 0.88 1.17E-08 0.58 0.20 PTPRC protein tyrosine phosphatase, receptor type, C IBD 16 [27] 0.69 0.047 0.7 0.039 0.78 2.00E-03 0.63 0.07 RGS2 regulator of G-protein signaling 2, 24kDa CU 46 [24] 0.71* 0.05* 0.9 2.79E-10 0.69 0.04 0.65 0.05 S100A9 S100 calcium binding protein A9 CD 37 [28] 0.77 0.042 0.95 <1E-16 0.88 4.40E-05 0.62 0.09 SELE selectin E IBD 16 [27] 0.73 0.09 0.91 4.74E-10 0.84 0.0003 0.56 0.28

B Gene Original study GSE42296in PBMC Sample biopsy datasets (n=3) Symbol Full name Disease Type of sample n Ref AUC p-value Average AUC Average p value C1R complement component 1, r subcomponent IBD serum 18 [29] 0.75 1.50E-03 0.72 0.06 MAP1LC3B microtubule-associated protein 1 light chain 3 beta CD peripheral 20 [26] 0.74 2.12E-04 0.69 0.02 WARS tryptophanyl-tRNA synthetase CD peripheral 20 [26] 0.71 7.10E-03 0.78 0.01 APOA4 Apolipoprotein A-IV IBD serum 18 [29] 0.7 1.24E-03 0.58 0.26 CA2 carbonic anhydrase II CD peripheral 20 [26] 0.69 1.40E-03 0.65 0.11 ODC1 ornithine decarboxylase 1 CD peripheral 20 [26] 0.69 1.76E-03 0.76 0.006 BMP6 bone morphogenetic protein 6 CD peripheral 20 [26] 0.69 1.82E-03 0.53 0.41 PBX1 pre-B-cell leukemia homeobox 1 CD peripheral 20 [26] 0.68 1.98E-03 0.64 0.12 CYP1B1 cytochrome P450, family 1, subfamily B, polypeptide 1 CD peripheral 20 [26] 0.65 4.64E-03 0.56 0.32

C   Source: biopsy Source: blood All published markers 65 39 Of these: validation in same tissue is OK 25 9 Of these: validation in different tissue is OK 3 3

Table 2: Detailed results for previously published biomarker candidates including characteristics of the original studies describing the marker as well as performance of the gene to discriminate responder and non-responder patients after infliximab therapy in each available dataset. Biomarkers identified in colon biopsy specimens (A) include genes with a p value <0.05 as the average of the three biopsy-based dataset is listed. Biomarkers identified in blood samples (B) and number of genes with a consistent discriminator performance in each dataset of the same type of sample (C). Ref #17 has more patients as in Table 1 because in the original study additional samples were included in the discovery set. *Genes identified in GSE12251 were also described in the paper where GSE12251 was published–these are included because their average p-value is significant in the two other datasets.