Systems approach for congruence and selection of cancer models towards precision medicine
Fig 5
Pathway- and gene-specific analysis for selection of representative cell line(s).
(A) Heatmap of pathway-specific deviance scores (DSpath) with 14 unbiased-selected and 1 manually-included pathways (30 < size < 200, |NES| > 1.5; shown on the rows) and 9 unbiased-selected and 1 manually-included cell lines (columns). The genome-wide SDA projected deviance score (DSSDA) is shown on the top side-bar and the pathway size and normalized enrichment score (NES) are on the left. Positive (negative) NES indicates up-regulation (down-regulation) in ILC compared to IDC. Average of the 14 pathways and the pre-selected “KEGG Cell Adhesion Molecules” pathway are shown at the bottom. The p-values of DSpath are annotated in the heatmap (one circle: p − value < 0.1; two concentric circles: p − value < 0.05; three concentric circles: p − value < 0.01), and smaller p-values indicate worse congruence. (B) Gene-specific heatmap shows DSgene for the 10 selected cell lines and 22 DE genes in “KEGG Cell Adhesion Molecules” pathway. (C) Part of KEGG PathView topological networks for BCK4 (DSpath = 1.323) for the “KEGG Cell Adhesion Molecules” pathway. The result shows discordance of 10 genes in BCK4 (orange stars showing up-regulation compared to ILC tumors and blue start showing down-regulation).