Fig. 3 | npj Systems Biology and Applications

Fig. 3

From: Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer

Fig. 3

Module biology and between cancer analysis identifies principles of gene co-expression. Heatmaps of gene signature enrichment between modules a BRCA, b CRC. Significant enrichment or depletion illustrated on red/blue scale, x-axis (modules) and y-axis (signatures). Hierarchical clustering according to gene signature enrichment (using top 15 signatures per module; FDR <0.05). Scalable version in Supplemental Fig. 11a, b. c, d Module relationship between cancers analyzed using hypergeometric test displayed as pairwise comparison matrix. Significance of overlap displayed as p-values on indicated color scale (p-values <0.001); overlap by c module gene membership, d enriched gene signatures. Gray side bars illustrate maximal significance for module match. Module class Cancer-Hallmark: gray, Cell-of-origin: blue, Chromosome-Region: cyan, Functional-Gene-Battery: yellow, Structural-Gene-Battery: orange and Unassigned: white (Scalable version in Supplemental Fig. 11c, d)

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