The dataset, DE_GSE8057, was derived from the GEO: GSE8057 dataset in the GEO database. The GSE8057 dataset contains expression data from ovarian cancer cells at multiple time points (0, 2, 6, and 24 h) and under two treatment conditions (cisplatin and oxaliplatin).38 The DE_GSE8057 dataset contains DEGs obtained from different treatments and time points versus control samples. Eight groups of DEG lists (specified by the formula Gene ~ Time + Treatment) were analyzed simultaneously using compareCluster with WikiPathways. The result (Figure 4) indicates that the two drugs have distinct effects at the beginning but consistent effects in the later stages. Several pathways including DNA damage and cell-cycle progression were perturbed by either cisplatin or oxaliplatin drug exposure. The finding is consistent with the discovery obtained by data-driven modeling.38data(DE_GSE8057)xx <- compareCluster(Gene∼time+treatment, data=DE_GSE8057, fun = enricher,TERM2GENE=wp[,c("wpid", "gene")], TERM2NAME=wp[,c("wpid", "name")])
