Supplementary Figures 1-16 from Improved Delineation of Colorectal Cancer Molecular Subtypes and Functional Profiles with a 62-Gene Panel

Abstract

<p>S1. Expression profiles of cell type-specific markers. S2. Example of a subnetwork consisting of 1000 samples from the original CMS dataset. S3. Robustness analysis of the 2-round network clustering method. S4. Hierarchical clustering of CMS2 samples. S5. Hierarchical clustering of CMS4 samples. S6. Agreement between original CMS and new intra-CMS subtypes. S7. Comparison of our gene panel with previously published panels for CRC. S8. Expression of 62-gene panel on CMS2/iCMS2 samples in the SG-Bulk cohort. S9. Expression of 62-gene panel on every epithelial cell from four selected patients from the iCMS cohort. S10. Progressive changes in inflammatory, immune, and proliferative pathway activities from CMS2 to CMS4 intra-subtypes. S11. Expression profiles of cellular senescence markers. S12. Mutation profiles and rates for KRAS, BRAF and PIK3CA. S13. Progressive changes in inflammatory, immune, and proliferative pathway activities between CMS1, CMS3, and CMS4 intra-subtypes. S14. Progressive changes in WNT, EMT, MAPK, and VEGF sub-pathway modules. S15. Expression profiles for JAK-STAT and amino sugar and nucleotide sugar metabolism pathways. S16. Confusion matrix for the classification of 7 intra-subtypes with an artificial neural network model.</p>