we developed an online transcriptome-based multi-scale network pharmacology platform (TMNP) for exploring the global effect of herbal medicine. Firstly, it is conceived to build specific functional gene signatures for different biological scales from molecular to higher tissue level. Based on these knowledge, TMNP uses pharmacotranscriptomics of herbal medicine as input and builds associations between herbs and biological scales to explore the multi-scale effects of herb medicine.
Helper_TMNP.R includes functions for multi-scale association analysis between query gene expression profiles and the curated gene signatures of different biological scales. Helper_plot.R includes functions for analysis plots. Data folder contains gene signatures for each scales, including target genes, pathways, biological processes, pathological processes, cells and tissues.