Bioinformatic analysis of Mayo PDX RNAseq data

We derived RNAseq RPKM expressions of Mayo PDX cells from Vaubel et al., 2020 [34 (link)] (19,552 genes in 20 MES patients, 16 PN patients, and 30 CL patients, www.cbioportal.org). We filtered out genes with geometric means small than 1 and with counts in less than 80% of patients, and added a pseudo count of 0.1, to achieve a normal gene expression distribution compared to original distribution (Figure S6a,S6b, 11752 genes left). We applied the two-sample t-test to the RNAseq-derived mRNA expression levels of Mayo MES and PN lines, and derived 1,177 differential genes with p<0.05 and FC>2 in the volcano plot (Figure S6c). We applied enrichment analysis in Gene Ontology (http://geneontology.org) [38 (link)] and derived 216 migration genes in “cell adhesion” and “cell motility” biological processes. We further applied the enrichment analysis and derived 23 actin genes (Figure 5a), 9 motor genes (Figure 5b), and 47 clutch (Figure 5c) genes in “actin cytoskeleton,” “actomyosin” coupled with “myosin II complex,” and “focal adhesion” cellular components, respectively.
We applied the correlation analysis between the mRNA expression ratios of the actin (Figure 5a), motor (Figure 5b), clutch (Figure 5c) genes in the 10 Mayo lines used in the present study (no mRNA data available for Mayo 16 line) and their CMS parameter values (v_poly, n_m, n_c), respectively. The correlation coefficients (R) of all the genes were sorted and plotted in Figure 5, with the significant correlation coefficients in red.
We applied Cox regression analysis between the mRNA expression ratios of the actin (Figure S7a), motor (Figure S7b), and clutch (Figure S7c) genes in a cohort of 66 Mayo patients and their overall survival, and their hazard ratios with 95% Confidence Interval were sorted and plotted in Figure S7, with the significant hazard ratios in red.