YInflammatory bowel disease (IBD) is an intractable chronic inflammatory disease with repeated remissions and relapses, but its pathophysiological mechanisms are unknown. In this study, we used dynamic network biomarker (DNB) analysis, which captures "biological fluctuations" at the critical point of state transition, to investigate the pathophysiology of inflammatory bowel disease (IBD). In the DSS colitis model, the colon was removed in time series and transcriptome analysis was performed. The results showed that the symptoms of colitis were remarkable after the 5th day, but DNB analysis of transcriptome profiling data revealed Mebyo, with many genes highly correlated and highly fluctuating on the 3rd day. Furthermore, a mathematical importance ranking was performed, and mast cell markers ranked highest, suggesting that mast cells may be a factor defining the unaffected state of colitis.