Figure 2. Biological description of biomarker groups.

(A) MsigDB gene set enrichment analysis using Reactome (R), KEGG (K), Biocarta (B), and PID (P) pathways (extracted from the MSigDB repository) for genes underlying biomarker group 1 and 2. (B) Physical and functional interaction network of genes upregulated in the predicted resistant PDX cluster (biomarker group 2). Functional interactions from ReactomeFI and physical interactions from Bioplex, IRefIndex, Mentha, HumanInteractome, and Human Protein Reference Database (HPRD). (C) As in B, physical and functional interaction network of genes downregulated in the predicted resistant PDX cluster (biomarker group 1). The size of the circles is proportional to the –log₁₀(P value) derived from a Student’s t test comparing 2 patient groups revealed by hierarchical clustering in Figure 1.