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Angelicae Sinensis Radix, also called Dang-Gui in Chinese, is an important and widely used natural product in traditional Chinese medicine (TCM) formulae with therapeutic properties of “menstrual regulation”. However, the underlying mechanisms on the molecular-interaction-level are still under exploration. In this study, based on evidenced bioactive compounds, targeted genes and proteins, different level functional annotations on gene ontology biological processes (GOBP) was deployed and then validated with microarray data. As a result, participating-fold analysis of targeted proteins revealed that the rhythmic process is the top GOBP. Further analysis indicated that the ovulation cycle process is associated with both the rhythmic process and TCM clinical relevance. After that, a kernel candidate regulation network was constructed towards the therapeutic properties of menstrual regulation identified in TCM that is delivered by Dang-Gui.

Ginseng is an important herbal medicine in traditional Chinese medicine (TCM) with therapeutic properties of “reinforcing primary qi” and “pulse restoring and blocking depletion” that are mentioned in both TCM textbooks and the Pharmacopoeia of the People’s Republic of China. However, the underlying mechanisms are still under exploration. In this study, based on evidenced bioactive compounds and targeted genes/proteins, top-level functional annotation towards gene ontology biological processes was deployed and then validated with transcript microarray data. As a result, a kernel candidate regulation network was constructed towards the therapeutic properties of ginseng identified in TCM. Functional annotation indicated three associated biological processes e.g. (1) cell killing, (2) rhythmic process, and (3) growth. In short, through regulating the three processes, the therapeutic properties of “reinforcing primary qi” and “pulse restoring and blocking depletion” identified in TCM can be roughly elaborated and validated.

Dioscoreae Rhizoma, also called Shan-Yao in Chinese, is a tonic food and herbal medicine in traditional Chinese medicine (TCM). Recent biomedical researches on Shan-Yao mainly focused on cancer and immune responses that are scattered in the literature. To build a holistic view of the immunoregulation functions delivered by Shan-Yao, the dispersed experimental knowledge items were collected, integrated, analyzed, and demonstrated. As a result, a candidate regulation network was constructed towards the immunoregulation. This network was composed of Shan-Yao, bioactive compounds, target proteins, protein interactions, pathway enrichment, and functional annotations. Functional annotations demonstrated the cell killing process is tightly associated with immunoregulation scenarios under different conditions via pathway enrichment, all are participated by the same target proteins of Shan-Yao.

Astragali Radix, called Huang-Qi in Chinese, is a widely used traditional Chinese medicine (TCM) with therapeutic effects of “tonifying qi” that is identified in both TCM formulae, textbooks, and the Pharmacopoeia of the People’s Republic of China. However, the underlying mechanisms of the bioactive compounds and target proteins are still under exploration. In this study, based on evidenced bioactive compounds and targeted genes/proteins, different level functional annotations towards gene ontology biological processes and KEGG pathways were deployed and validated. As a result, the candidate molecular regulation network was constructed towards the “tonifying qi”. Functional annotation indicated one outstanding biological process called cell killing which is tightly associated with immunoenhancement. In short, the “tonifying qi” effect identified in TCM on Astragali Radix might be associated with immunoenhancement by various modern bio-medical studies.