Gegen Qinlian Decoction Attenuates Ulcerative Colitis by Inhibiting PANoptosis: A Multi-Omics and Experimental Study

We present an integrated bioinformatics and network pharmacology protocol to clarify the therapeutic mechanisms of Gegen Qinlian Decoction (GQD) in ulcerative colitis (UC), with a particular focus on PANoptosis-related regulation. This protocol is designed to systematically identify potential bioactive compounds, therapeutic targets, signaling pathways, and immune-related mechanisms through multi-database mining and transcriptomic analysis. Gene expression profiles from UC cohorts, including GSE87466 and GSE92415 from the GEO database, are analyzed using differential expression analysis and weighted gene co-expression network analysis to identify disease-related genes. Candidate targets of GQD are collected from public pharmacology databases and intersected with UC- and PANoptosis-associated genes to determine core therapeutic targets. Protein-protein interaction network construction, enrichment analyses, and compound-target-pathway network modeling are then performed to reveal the molecular basis of GQD activity. In addition, immune infiltration analysis is incorporated to explore the relationship between key genes and the intestinal immune microenvironment. Molecular docking is further used to evaluate the binding potential between major active compounds and hub targets. This protocol provides a reproducible, systematic framework for investigating how GQD alleviates UC by modulating PANoptosis and related inflammatory pathways, and may serve as a useful reference for mechanistic studies of other traditional Chinese medicine formulas in complex inflammatory diseases.