Mechanistic Study of a Patent Formula of Deer Antler and Ginseng in Triple-Negative Breast Cancer: Research Based on Bioinformatics and In Vivo Experiments

This collection contains all raw and processed data supporting the investigation of the traditional Chinese medicine (TCM) formula DAGF (Drug-Administered Gastrodia Formula) as a potential anti-TNBC agent. The dataset is organised into five modules: Putative target list of DAGF – 1,927 candidate proteins retrieved from the TCM Systems Pharmacology Database (TCMSP) after oral bioavailability (OB ≥ 30 %) and drug-likeness (DL ≥ 0.18) filtering. Protein–protein interaction (PPI) network – constructed by mapping the above targets to STRING v11.5 (confidence score ≥ 0.7) and visualised in Cytoscape 3.9.1; edge and node tables are provided. Functional enrichment results – Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses performed with clusterProfiler (p-adjust < 0.05, q < 0.2); top 30 GO-BP terms and 20 KEGG pathways are reported together with full enrichment tables. Chemical profiling of DAGF – LC-MS/MS raw files (.raw and .mzML) acquired on a Q-Exactive HF-X mass spectrometer (Thermo) in both positive- and negative-ion modes, accompanied by the identified compound list (level-1 annotations against MassBank, GNPS, and TCM-library; MS-DIAL v4.90). TNBC-specific target library – 2,104 genes associated with triple-negative breast cancer downloaded from GeneCards (relevance score ≥ 5) and used for intersection analysis with DAGF targets. These files enable reproducibility of the network pharmacology pipeline and provide a comprehensive chemical and biological reference for researchers exploring TCM-based TNBC therapeutics.