Figure 5 — Ulcerative Colitis SNP-Propagated Signalling Network and Pathway Analysis

Panel A — SNP-Propagated Signalling Network
	•Software: Cytoscape
	•Cytoscape session: UC_ppi_network_10k.cys
	The network modules are annotated based on REactome enrichmnet stored in Dataset EV2.


Panel B — Protein Frequency Distribution
	•Input file: uc_only_ppi_10k.txt
	•Script: Figure5_b.rmd
	•Description: Frequency distribution of SNP-propagated proteins across UC patients.

Panel C — Reactome Pathway Enrichment
	•Input files:
		•uc_only_ppi_10k.txt
		•ReactomePathways.gmt
		•OmniPath_27_10_2021_directed.ncol (reference signalling network for background (universe)
	•Output file: Reactome_UC_PPI_100_cutoff_ora_results.csv
	•Description: Reactome over-representation analysis (ORA) of commonly perturbed proteins (present in ≥100 patients).