Figure 7

Agreements of different types of significant markers. The agreements of three different types of significance markers between two data sets: ‘GPF classifier’ denotes pathway features obtained by GSEA, and ‘GLEG classifier’ denotes leading edge gene markers determined by GSEA. ‘SG classifier’ and ‘SKG classifier’ denote the genes determined by Fisher selection from full gene expression profiles and restricted to the set of KEGG pathway genes, respectively, with feature numbers controlled to 20% of each population. ‘SG_random’ denotes gene sets selected randomly (again to 20% of the full gene set) from full gene expression profiles. ‘Ovarian_Stage’ denotes the ovarian stage data sets (marker stability compared between BI and UNC data), ‘Ovarian_SUR’ denotes ovarian survival data sets (BI vs. UNC), and ‘Metastasis’ denotes metastatic breast cancer data sets (based on the Wang and van de Vijver data sets). For each pair of datasets, overlapping biomarkers were all extracted from matching based on the top 40 pathways in each. Vertical axis represents biomarker consistency as the quotient formed by the size of the intersection of the two biomarker sets, divided by the size of their union.