TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine

Area of Science:

• Pharmacology
• Bioinformatics
• Systems Biology

Background:

• Understanding the global effects of herbal medicine is challenging due to complex compositions.
• Current chemo-centric network pharmacology relies on chemical ingredients, limiting holistic analysis.
• Gene-expression profiles offer a comprehensive view of biological responses to herbal treatments.

Purpose of the Study:

• To develop an online transcriptome-based multi-scale network pharmacology platform (TMNP).
• To explore the global and multi-scale effects of herbal medicine.
• To integrate herbal medicine with multiple biological scales for a systems-level understanding.

Main Methods:

• Constructing functional gene signatures across molecular to tissue levels.
• Developing algorithms to correlate transcriptional profiles with gene signatures.
• Utilizing pharmacotranscriptomics as input for TMNP to link herbs with biological scales.

Main Results:

• Demonstrated the platform's capability using Astragalus membranaceus and Xuesaitong injection.
• Revealed multi-scale effects of herbal medicine through pharmacotranscriptomics.
• Successfully integrated herbal medicine and biological scales within a unified framework.

Conclusions:

• TMNP extends conventional network pharmacology by incorporating transcriptome-wide effects.
• The platform provides a novel approach to observe complex herb-human interactions.
• TMNP offers a valuable tool for advancing herbal medicine research and application.