227 Interleukin−6 signaling Mitotic Anaphase Cell Cycle Checkpoints Interleukin−12 family signaling Chemokine receptors bind chemokines Mitotic Metaphase and Anaphase Transcriptional regulation by RUNX3 RAF−independent MAPK1/3 activation Antigen processing−Cross presentation Collagen formation Interferon alpha/beta signaling Interferon Signaling Integrin cell surface interactions Interleukin−10 signaling Immunoregulatory interactions between a Lymphoid and a non−Lymphoid cell Interferon gamma signaling Extracellular matrix organization Neutrophil degranulation Interleukin−4 and Interleukin−13 signaling Signaling by Interleukins 0.00 0.02 0.04 0.06 ratio Description 2e−04 4e−04 6e−04 qvalue Cell surface interactions at the vascular wall Peptide ligand−binding receptors Interleukin−6 family signaling Assembly of collagen fibrils and other multimeric structures Dectin−2 family Collagen formation Antigen Presentation: Folding, assembly and peptide loading of class I MHC Collagen degradation Immunoregulatory interactions between a Lymphoid and a non−Lymphoid cell Chemokine receptors bind chemokines Degradation of the extracellular matrix Interferon Signaling Integrin cell surface interactions Interferon alpha/beta signaling Interferon gamma signaling Extracellular matrix organization Interleukin−10 signaling Neutrophil degranulation Interleukin−4 and Interleukin−13 signaling Signaling by Interleukins 0.000 0.025 0.050 0.075 ratio Description 1e−04 2e−04 3e−04 4e−04 qvalue Post−translational protein phosphorylation Interferon gamma signaling Metabolism of water−soluble vitamins and cofactors Collagen formation Regulation of Insulin−like Growth Factor (IGF) transport and uptake by Insulin−like Growth Factor Binding Proteins (IGFBPs) Integrin cell surface interactions Interferon alpha/beta signaling ECM proteoglycans Collagen degradation Acyl chain remodelling of PC Non−integrin membrane−ECM interactions MET promotes cell motility Interleukin−10 signaling Signaling by Interleukins MET activates PTK2 signaling Degradation of the extracellular matrix Laminin interactions Interleukin−4 and Interleukin−13 signaling Extracellular matrix organization Neutrophil degranulation 0.00 0.02 0.04 0.06 0.08 ratio Description 2e−04 4e−04 6e−04 qvalue Ileum tissue: non-IBD vs. CDnon vs. CDi Colon tissue: non-IBD vs. CDnon vs. CDi Colon tissue: non-IBD vs. UCnon vs. UCi Extended Data Figures Extended Data Figure S1 Extended Data Figure S1 | Analysis of pathways associatedwith each comparative gene expression analysis. The main pathways associated with inflamed ileal tissue in patients with CD (blue) include neutrophil degranulation, extracellular matrix (ECM) organization and IL-4/IL-13-signaling. Similar pathways were overexpressed in inflamed colonic tissue from patients with CD (green), but with a more prominent contribution from interleukin signaling pathways. Interleukin signaling pathways were also dominantly expressed in inflamed colonic tissue from patients with UC (orange), with other pathways expressed including neutrophil degranulation, ECM pathways, interferon gamma signaling and immunoregulatory interactions between lymphoid and non-lymphoid cells. Pathways were annotated using the Reactome pathway database. Abbreviations: CDi, inflamed tissue from patients with Crohn’s disease; CD-non, noninflamed tissue from patients with Crohn’s disease; UCi, inflamed tissue from patients with ulcerative colitis; UC-non, non-inflamed tissue from patients with ulcerative colitis.
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