Figure 3 from Identification of a Two-Gene Biomarker Correlated with Sensitivity to Combined PARP7 Inhibition and AHR Activation in Cancer Cells

Synergistic cancer cells have unique transcriptional and proteomic characteristics. A, Bar plot of HALLMARK pathways (P < 0.05) identified in ORA of 588 upregulated (FC > 2 and adjusted P < 0.05) and 154 downregulated (FC < 0.5 and adjusted P < 0.05) genes in synergistic cell lines compared with nonsynergistic cell lines. B, Scatter plot showing the median values of RPPA protein expression levels in synergistic vs. nonsynergistic cell lines. Proteins with higher expression in synergistic cell lines are highlighted in red whereas those more highly expressed in nonsynergistic lines are shown in blue. C, Dendrogram of co-expressed gene modules identified by WGCNA using the 1,000 most variable genes across 27 synergistic and 10 nonsynergistic cell lines. Genes were grouped into nine distinct modules based on expression similarity. Unassigned genes are shown in gray. D, Bar plots showing the five TFs most significantly associated with the regulation of module 3. TFs are ranked by P value with the most significant shown on the top.