Fig. 3: Transcriptomic analysis demonstrated distinct mRNA expressional patterns according to different clonality.

Related to Supplementary Fig. 4 and Supplementary Data 3. a Gene Set Enrichment Assay (GSEA) analysis using normalized transcripts of all genes (n = 35,993) of tumor tissues and corresponding derivatives compared to the normal tissue. The KEGG signaling pathway pathways are categorized and indicated with representative colors. A total of overlapped 50 pathways that were enriched in both tumors and PDOs were selected to identify the differentially expressed pathway between samples (red, upregulated; blue, downregulated). b Sample to sample distances of mRNA expressions of all genes (n = 35,993) among tumor tissues (n = 6) and corresponding derivatives (n = 18) based on hierarchical clustering. Each cluster is marked with representative colors. The intact cluster of organoids was adjacent to the original tumors in Euclidean distance. c Principle component analysis (PCA) using values of normalized transcripts indicates tumor site D and E from the rest with principle component 1 (PC1) whereas principle component 2 (PC2) divided PDOs from tissue. Top 10% contributing variables in PC1 are indicated on the top of the PCA plot. d Gene Ontology of the top 5% genes contributing to the distinction of C- and F-TO from the rest (PC1) was performed with P-value < 0.05 as a cutoff. Among the selected 21 pathways in gene sets of the Reactome database, five enriched biological processes (p-value < 2.16E−05) were indicated in cnetplot.