Fig. 3

Identification and characterization of differentially expressed gene sets in KRAS (G13C) iPSC-HPCs. a A heatmap demonstrating a set of differentially expressed genes (DEG) between wild-type (WT) and KRAS-mutant (Mut) HPCs after 7-day culture. Data from each patient are clustered separately (Pt 1 and Pt 2). Two samples cultured with different cytokine conditions (SF and STF3) are treated as a pair within each cell type. A cut-off value of an FDR (false-discovery rate) < 0.1 and a minimal log2 fold change of 1.5 are used. The gene sets found down-regulated in Mut groups are shown at the top, whereas those up-regulated are at the bottom. b An MA plot depicting DEGs. Several genes of interest are indicated with the enlarged symbols in both up-regulated (red)- and down-regulated (blue)-gene sets. c–e Enrichment analysis for the DEGs in specified gene sets. Shown are adjusted P values (adj. P val) and the number of genes (nGenes) contained in each pathway group. The pathway databases used are KEGG (c, Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), Biological Process (d), and Hallmark. MsigDB (e, The Molecular Signatures Database)