Abstract
BACKGROUND: Traditional Chinese Medicine (TCM) prescriptions are complex, multi-botanical drug systems in which dosage critically influences therapeutic efficacy. While network pharmacology is widely used to analyze TCM mechanisms, existing methods ignore the dosage of botanical drugs, a key limitation that may skew predictions. This study investigates how integrating dosage data alters network analysis outputs, addressing a fundamental gap in understanding TCM's dosage-dependent effects. METHODS: Our analysis compared dosage-weighted and traditional non-dosage network approaches across 94 traditional Chinese medicine (TCM) prescriptions. We developed four custom indicators to quantify differences throughout the network pipeline: Dedis (input distance difference), DeSD (input standard deviation difference), DeDT (drug target prediction difference), and DePy (pathway prediction difference). The interrelationships among these indicators were examined to indicate when dosage adjustments influence predictions. A detailed case study further demonstrated the impact of dosage modifications on predictive outcomes. RESULTS: Among the indicators with inputs difference, Dedis, but not DeSD, exhibited a statistically significant relationship with output predictions, with target differences (DeDT) ranging from 0% to 68.9% and pathway differences (DePy) ranging from 0% to 74.6%. The interrelationships between these indicators were visualized using a clock model representation. The case study further demonstrated the impact of dosage on network outputs, revealing dosage refined both the predicted drug targets for individual botanical drugs and the subsequent pathway analysis results. CONCLUSION: Our study demonstrated that dosage significantly influences the outcomes of network analysis, with Dedis serving as a reliable indicator of whether such changes would occur. Specifically, changes resulting from dosage-dependent refinement of both drug target prediction and pathway analysis were observed.