Figure 5
Pathway modularity. Fraction of internal edges (within pathway; PK IN /PK T ) for 128 curated pathways (blue) vs. the distribution as expected by chance for randomized pathways (black) (A). The shift is statistically significant (P < 10-18) indicating a high level of modularity on average across pathways. (B) Average modularity (M; see Methods for mathematical definition) of pathways derived from the 6 pathway databases (columns) using edges derived from the 7 interaction databases plus the Ensemble network (rows), represented as a hierarchically clustered heatmap. (Bii) Corresponding P-values based on the Mann–Whitney U-Test. Note the heterogeneity; some pathway databases are highly modular regardless of interaction source, while others are less so.