2.5. BATMAN-TCM

BATMAN-TCM is a Bioinformatics Analysis Tool for Molecular Mechanism of Traditional Chinese Medicine and is the first online bioinformatics analysis tool specially designed for the study of molecular mechanism of TCM. It mainly performs TCM ingredients' target prediction and the subsequent network pharmacology analyses of the potential targets, aiming to improve the understanding of the “multicomponent, multitargets, and multipathway” combinational therapeutic mechanism of CMM. For each ingredient of CMM, BATMAN-TCM ranks its predicted candidate targets according to the order of decreasing score given by the target prediction algorithm for the drug-target interaction prediction. It uses a similarity-based method to predict the potential targets of CMM ingredients. The core idea of this method is to rank potential drug-target interactions based on their similarity to the known drug-target interactions. If the score of a candidate target ≥ “score cutoff”, then this target will be taken as the potential target of the ingredient investigated [6].

In BATMAN-TCM, herb list was selected and the 12 key CMM combinations mined out from DPTM were input into the platform. Score cutoff was set at 80 and adjusted P-value was set at 0.05. BATMAN-TCM first predicted the potential targets of each ingredient of CMM investigated and then performed functional analyses of these targets including Gene Ontology (GO), KEGG pathway, and OMIM/TTD disease enrichment analyses. CMM ingredient-target-pathway/disease association network and biological pathways in which CMM's targets are significantly enriched were also shown.