Figure 3.

Subtype-specific gene expression differences overlap highly with patient metastasis versus paired primary differences

(A) Schematic of gene set comparisons. For each PDX-based subtype, the set of genes high within that subtype versus the rest of the PDX tumors was overlapped with the set of genes high in patient metastases of the same PDX-based subtype versus the corresponding paired primaries. A top set of 1,133 genes involves significant gene set overlaps between PDX comparisons and paired patient metastasis comparisons for the same subtype, involving each of the four subtypes.

(B) Significance of overlap between the genes high within each of the PDX-based subtypes (using t test, p < 0.01, based on analysis of PDX compendium) and the genes high within paired patient metastasis versus primary within each subtype (p < 0.01, paired t test, based on analysis of the patient tumor metastasis compendium). Overlap p values were found by one-sided Fisher’s exact test or chi-square test. From these results, a set of 1,133 genes involves significant gene set overlap (p < 1E−6) for the same subtypes (e.g., 535 overlapping s1–s1 genes, 161 s2–s2 genes, etc.).

(C) Differential expression patterns for the top set of 1,133 genes involving significant gene set overlaps for any of the four PDX-based subtypes are shown across the PDX compendium dataset (differential expression relative to other tumors), patient tumor metastases compendium dataset (relative to other tumor metastases), and patient tumor metastasis versus paired primary compendium dataset (relative to primary pair). Subtype-specific expression patterns are highlighted. Selected genes of interest from the 1,133 genes are also represented individually by differential patterns.