Modulome-Fangjiome Association Study (MoFAS) reveals differential target distribution among four similar fangjis (formulas)

Ethnopharmacological relevance Precise target distribution is a key issue for further appropriate applications of fangjis (formulas) with similar efficacy and herbal constituents to maximize efficacy and minimize toxicity. Aim of the study To develop an algorithm for investigating the differential target distributions and characteristic mechanisms of fangjis. Main methods In this study, we proposed a Modulome-Fangjiome Association Study (MoFAS) for comparing fangjis from qi-invigorating and xue-nourishing fangjiome (represented by four fangjis: FEJ, SDT, LYG and QOL). Firstly, the database-driven target network of these 4 fangjis was constructed as qi-xue network and decomposed into modules. Then, the modular map with functional landscape were constructed based on consistency score and enrichment analysis. Finally, we employed a targeting rate (TR) matrix to assess the contribution of this fangjiome to modulome (a set of modules) and compared characteristic effect of fangjis by principal component analysis (PCA). Results A qi-xue network constituted by 579 proteins and 23 modules were constructed. In the functional landscape, 3 primary modules were mainly involved in the endocrine system and environmental adaptation. For the target distribution, SDT and QOL were more similar; the FEJ and LYG were located distant from other fangjis according to PCA. The common effects of FEJ, SDT, and QOL focused on stress response and organism development in environmental perturbation, but the FEJ was superior in regulating critical targets, primarily focusing on hormone and neurotransmitter processes. SDT and QOL were concentrated on the majority scale of the qi-xue network, especially for the mitotic cell cycle and development. LYG only targeted lymphocyte costimulation and icosanoid biosynthetic processes. Conclusion In this study, for the first time, we investigated the difference in the target distribution of qi-invigorating and xue-nourishing fangjiome and provided direct evidence for the characteristic therapeutic effect of these fangjis, which may promote the precise application of fangjis and support the identification of appropriate populations.