191 ● ● −100 −50 0 50 100 −100 0 100 PC1 PC2 Location_rough ● ● colon ileum PC1 (P=2.87x10-12) PC2 (P= 3.42x10-16) A C A B C 1013 (12.9%) 67 (0.9%) 2656 (33.9%) 34 (0.4%) 669 (8.6%) 1944 (24.8%) 1441 (18.4%) Ileum: Non-IBD vs. CDnon vs. CDi Colon: Non-IBD vs. CDnon vs. CDi Colon: Non-IBD vs. UCnon vs. UCi B PC1 (P= 7.15x10-27) PC2 (PKruskal-Wallis =3.78 x10-9) ● ● ● −100 −50 0 50 100 −100 0 100 PC1 PC2 Inflammation ● ● ● 1 2 3 Colon Ileum Non-IBD IBD non-inflamed IBD Inflamed PC1 (P=0.067) PC2 (P= 2.14x10-16) ● ● ● −100 −50 0 50 100 −100 0 100 PC1 PC2 Diagnosis ● ● ● CD Control Non-IBD CD UC ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1 2 3 1 2 3 1 2 3 2 3 4 JAK2 Ileum CD FDR =5.23 x10-16 Colon CD FDR =1.20 x10-17 Colon UC FDR =2.70 x10-30 FDR =9.48 x10-12 FDR =1.69 x10-13 FDR =1.44 x10-24 FDR =4.68 x10-28 FDR =7.51 x10-10 FDR =8.61 x10-17 FDR =8.87 x10-04 FDR =1.49 x10-11 FDR =1.16 x10-27 ● ● ● ●● ● ● ● ● 1 2 3 1 2 3 1 2 3 0 5 DUOX2 ● ● ● ● ● ● ● 1 2 3 1 2 3 1 2 3 0.0 2.5 5.0 7.5 MUC1 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 1 2 3 1 2 3 1 2 3 −4 −2 0 2 IL17A ● ● ● ● ● −1.0 −0.5 0.0 0.5 1.0 1.5 CD UC HEY1 ● ● ● ● ● −2 −1 0 1 CD UC HDAC9 ● ● ● ● ● −5.0 −2.5 0.0 2.5 CD UC VNN1 ● ● ● ● 0 5 10 CD UC APOB FDR =0.0093 FDR =0.001 FDR =7.81 x10-06 FDR =0.0071 IRE1alpha activates chaperones SLC transporter disorders Biological oxidations Disorders of transmembrane transporters Cellular hexose transport Plasma lipoprotein assembly, remodeling, and clearance Metabolism of fat−soluble vitamins Transport to the Golgi and subsequent modification SLC−mediated transmembrane transport Metabolism of vitamins and cofactors 0.00 0.02 0.04 ratio Description 1.6 1.7 1.8 −log10(qvalue) Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer Constitutive Signaling by NOTCH1 PEST Domain Mutants Signaling by NOTCH1 in Cancer Signaling by NOTCH1 PEST Domain Mutants in Cancer GAB1 signalosome PI3K events in ERBB2 signaling Notch−HLH transcription pathway Reversible hydration of carbon dioxide Signaling by NOTCH1 NOTCH1 Intracellular Domain Regulates Transcription 0.00 0.01 0.02 0.03 ratio Description 1.6 1.7 1.8 1.9 2.0 −log10(qvalue) Pathways enriched in CD inflamed colon Pathways enriched in UC inflamed colon D E Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer Constitutive Signaling by NOTCH1 PEST Domain Mutants Signaling by NOTCH1 in Cancer Signaling by NOTCH1 PEST Domain Mutants in Cancer GAB1 signalosome PI3K events in ERBB2 signaling Notch−HLH transcription pathway Reversible hydration of carbon dioxide Signaling by NOTCH1 NOTCH1 Intracellular Domain Regulates Transcription 0.00 0.01 0.02 0.03 ratio Description 1.6 1.7 1.8 1.9 2.0 −log10(qvalue) IRE1alpha activates chaperones SLC transporter disorders Biological oxidations Disorders of transmembrane transporters Cellular hexose transport Plasma lipoprotein assembly, remodeling, and clearance Metabolism of fat−soluble vitamins Transport to the Golgi and subsequent modification SLC−mediated transmembrane transport Metabolism of vitamins and cofactors 0.00 0.02 0.04 ratio Description 1.6 1.7 1.8 −log10(qvalue)
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