B. REACTOME Down Syndrome AML vs 1000 GBM vs 1000 OVC vs 1000 Bock hESC vs Wild-type Comparison Genomes Genomes Genomes vs iPSC iPSCs Number of Genes 8944 8970 8986 7554 7000 Variability Statistic MAD MAD MAD MAD SD Significant Variability 447 296 344 39 57 Pathways Significant Mean 714 711 713 3 12 Pathways Intersection of Mean ∩ 446 292 342 1 1 Variability Significant for 1186 1188 1189 0 187 GSEAlm Intersection of 263 179 204 0 5 GSEAlm Variability ∩ Significant for GSEA 169 32 24 3 4 (limma P-value) Intersection of GSEA P-value) 24 8 8 0 0 ∩ Variability S10. Top ten statistically significant KEGG pathways (adjusted P-value < 0.01) in the two-group cancer versus normal comparisons. We report the top ten pathways or all the significant pathways if there were less than ten for A. AML vs 1000 Genomes, B. GBM vs 1000 Genomes, C. OVC vs 1000 Genomes. Blue cells denote terms that were observed for both the variability-based and average expression-based analyses. Yellow cells denote pathVar terms that were unique to either the variability-based or average expression-based analysis. pathVar A. AML vs 1000 Genomes. MAD Mean B. GBM vs 1000 Genomes MAD Mean OVC vs 1000 Genomes C. MAD Mean
B. REACTOME Comparison AML vs 1000 Genomes GBM vs 1000 Genomes OVC vs 1000 Genomes Bock hESC vs iPSC Down Syndrome vs Wild-type iPSCs Number of Genes 8944 8970 8986 7554 7000 Variability Statistic MAD MAD MAD MAD SD Significant Variability Pathways 447 296 344 39 57 Significant Mean Pathways 714 711 713 3 12 Intersection of Mean ∩ Variability 446 292 342 1 1 Significant for GSEAlm 1186 1188 1189 0 187 Intersection of GSEAlm ∩ Variability 263 179 204 0 5 Significant for GSEA (limma P-value) 169 32 24 3 4 Intersection of GSEA P-value) ∩ Variability 24 8 8 0 0 S10. Top ten statistically significant KEGG pathways (adjusted P-value < 0.01) in the two-group cancer versus normal comparisons. We report the top ten pathways or all the significant pathways if there were less than ten for A. AML vs 1000 Genomes, B. GBM vs 1000 Genomes, C. OVC vs 1000 Genomes. Blue cells denote terms that were observed for both the variability-based and average expression-based pathVar analyses. Yellow cells denote terms that were unique to either the variability-based or average expression-based pathVar analysis. A. AML vs 1000 Genomes. MAD Mean B. GBM vs 1000 Genomes MAD Mean C. OVC vs 1000 Genomes MAD Mean