Additional file 6.

The relationship between module size and gene ontology enrichment p-values in 8 real data applications. In each panel, module size (x-axis) is plotted against −log10 GO enrichment p-values (y-axis)in dots. Loess regression lines are provided to show the trend. Red and black color represent network modules constructed using TOM and AMI,UniversalVersion2 based measures, respectively. In most data sets, the enrichment of modules defined by TOM is better than that of comparably sized modules defined by AMI,UniversalVersion2.

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Song et al. BMC Bioinformatics 2012 13:328   doi:10.1186/1471-2105-13-328