Gene Expression Profiling and Pathway Network Analysis Predicts a Novel Antitumor Function for a Botanical-Derived Drug, PG2

Figure 1

Schematic illustration of using PG2 gene signatures to infer PG2 quality and consistency, as well as the pathways induced by PG2. ComBat package was used to adjust the batch effect before analyzing expression profiles. To elucidate the consistency of three PG2 preparations, additional small molecule drugs and herbal extracts were included to test whether they are similar between each preparation according to correlation coefficient. Analysis of gene expression profiling, limma, t-test, topological clique, and fold-change cut-off analyses were used to identify the PG2-enriched signature. Chemical-protein interaction analysis via STITCH reveals a link between doxorubicin and PG2. Moreover, most of the immune-related pathways were retrieved from CPDB using the PG2-enriched signature. Finally, using the Connectivity Map tool, which used ranking by KS enrichment scores, two drugs were identified (withaferin A and parthenolide) that exhibit gene signatures similar to the PG2-enriched signature.