Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples
Fig 6
FOXM1 was revealed as a key gene underlying breast cancer progression by PROB.
The gene expression data of 196 patients with clinical information (e.g., grade) were extracted from the GEO database (GSE7390 [40]). (a) Heatmap showing the expression profile of 100 selected genes that were most sustainably ascending (blue group) or descending (purple group) during cancer progression. (b) Gene set enrichment analysis for the descending genes (upper panel) and ascending genes (lower panel). The descending genes were enriched in local movement processes, and the ascending genes were mainly enriched in cell cycle and cell division processes. (c) The inferred GRN for the 100 genes. FOXM1 was found to be a hub gene in the network. (d-f) Clinical relevance of FOXM1 for breast cancer patients with respect to distant metastasis-free survival (DMFS) (d), relapse-free survival (RFS) (e) and overall survival (OS) (f). (g) Significance test of the prognostic power of FOXM1 using a bootstrapping approach. The p value from the permutation test was 0.0146, verifying the statistical significance of the prognostic power of FOXM1.