Fig. 2

Transcriptomic Characterization of the Engineered Model in the Context of Available CRC References. a Gene expression heatmap displaying the relative expression of 260 differentially expressed genes (DEGs) between normal intestinal epithelial stem cells (WT) and engineered CRC model cells (AKTS). b UMAP embedding of MOBER-derived transcriptomic data integrating engineered CRC models with publicly available CRC datasets. Two primary clusters were identified: Cluster 1, comprising metastatic CRC samples, primary tumors, and most CRC cell lines; and Cluster 2, which includes the engineered CRC models grouped with primary CRC tissues and a subset of metastatic samples. Insets (2A, 2B) highlight the clustering of healthy intestinal stem cells with public healthy tissue samples (2A) and the engineered CRC models with primary CRC tissues (2B). c Differential gene programs identified using ExpiMap overlaid on the clustered data from engineered CRC models and publicly available RNA-seq datasets. Gene programs were derived from GSEA collections, identifying pathways relevant to CRC progression and differentiation.