Figure 5
Impact of IBD on signalling leading to wound healing in colonic mucosa. The subgraph extracted from the merged IBD network model shows the iNode enrichment score for each node when the model is scored with comparative transcriptomic data from IBD-affected versus healthy control samples. The values are not comparable between the graphs, and the scale is adjusted on the basis of the highest value for each node. Most intermediate nodes that were not scored have been removed for simplicity (The complete results are in Supplementary file 1). The iNodes leading to “programmed cell death” are shown in Figs. 3 and 6. Black outlines indicate nodes that were significantly impacted in both CD and UC samples; blue outlines indicate nodes that were significantly impacted in CD samples; and purple outlines indicate nodes that were significantly impacted only in UC samples. The directionalities are shown as yellow or turquoise bars for inferred upregulation or downregulation, respectively. The order is as follows: 1) CD and 2) UC. Abbreviations: act, protein activity; p, protein abundance; bp, biological process. HGNC is the namespace for human proteins; GOBP is the namespace for biological processes; MESHD is the namespace for diseases; and GOCC is the namespace for complexes. SFAM and PMIBP are custom namespaces for protein families and biological processes, respectively. The figure was created using Cytoscape v3.7.1 (https://cytoscape.org). The Cytoscape graph was then exported to pdf and the layout was further modified for better readability in Adobe Illustrator 2019 (https://adobe.com).
