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. 2022 Aug 31;11:e78012. doi: 10.7554/eLife.78012

Figure 2. Treatments elicit cell-specific transcriptional changes.

(A) An overview of the applied workflow for the RNA-seq analysis. (B) Number of up- (red) and down-regulated (blue) differential expression (DE) genes in BxPC-3 and HCT-15 cells after treatment with M (10 nM), B (200 nM), or DMSO 0.5% (ctrl) for 6 hr and 12 hr (adjusted p threshold = 0.05, shrinkage = TRUE, and multiple testing method = independent hypothesis weighting [IHW]). (C) Gene ontology (GO) database functional enrichment gene set enrichment analysis (GSEA) on cell-specific and shared up- and down-regulated DE genes. For each identified biological process, enrichments in terms of count and p-value of representative terms are reported (p<0.05). (D) Expression level of cell-specific 6 hr DE genes across test conditions. GSEA was performed on modules with similar regulation identified by hierarchical clustering: for each cluster, representative GO terms and genes of the associated load are reported.

Figure 2.

Figure 2—figure supplement 1. Treatments elicit cell-specific transcriptional changes—supporting data.

Figure 2—figure supplement 1.

(A) Scheme of the applied workflow for the RNA-seq analyses. (B) Principal component analysis (PCA) post surrogate variable analysis (SVA) batch correction of RNA-seq data: PC1 vs PC2 showed sample separation by cell line, PC2 vs PC3 (cell lines depicted separately) showed treatment and time point separation. (C) Volcano plots reporting up- and down-regulated differential expression (DE) genes in all treated vs control comparisons (adjusted p<0.05). (D) Venn plot reporting the number of specific and shared up- and down-regulated DE genes between BxPC-3 and HCT-15 cells (union of DE genes in all treated vs control comparisons). (E) Enriched gene ontology (GO) terms (p<0.05) derived from gene set enrichment analysis (GSEA) on BxPC-3 and HCT-15 DE genes (union of DE genes in all treated vs control comparisons) and on shared DE genes (up- and down-regulated separately). (F) Schematic representation of enrichment map-based selection of representative GO terms to be reported in Figure 2C.
Figure 2—figure supplement 2. Treatments elicit cell-specific transcriptional changes—supporting data 2.

Figure 2—figure supplement 2.

(A) Expression level of cell-specific 12 hr differential expression (DE) genes across test conditions. Gene set enrichment analysis (GSEA) was performed on modules with similar regulation identified by hierarchical clustering: for each cluster, representative gene ontology (GO) terms and genes of the associated load are reported. (B) GO database functional enrichment (GSEA) obtained from log2FC ranks in all treated vs control comparison both in BxPC-3 and HCT-15 cells. For each identified biological process, enrichments in terms of absolute normalized enrichment score (abs[NES]) and -log(p) of representative terms are reported (p<0.05).