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Figure 2 | BMC Bioinformatics

Figure 2

From: Inferring functional modules of protein families with probabilistic topic models

Figure 2

Overview of the STRING-based evaluation of 198 modules. We evaluated 198 PF-modules from a randomly chosen run with k = 200. Coverage values for the modules serve to assess their functional coherence. A coverage value of 100% means that the complete OG set of a module is interconnected within the reference functional network and forms a single cluster therein. If the coverage is 50%, then the same holds for half of the OGs of a module. The plot shows coverage values for all 198 modules of the exemplary run (modules 'ChemoTax', 'Flagell' and 'VitB12' are discussed in detail in the Results section). 'Verified-PWF-couplings': The percentage of verified pairwise functional couplings with respect to all tested OG pairs of a module. 'Verified-PWF-couplings + Verified-TRF-couplings': The percentage of a module's OG pairs that are either verified pairwise couplings or verified first-order transitive functional couplings. 'Expected verified F-couplings': The expected percentage of verified pairwise couplings to be found by chance for the OG set of a module. For an average-sized module, we expect to obtain less than one (E[h] = 0.19) verified pairwise functional coupling by chance. The dashed lines indicate mean values, and the averaged mean coverage over all nine runs is 57.9% (1.3% s.d.). Finally, we determined the fraction of OG pairs within a module which are verified and have also been predicted by the pairwise co-occurrence method used by STRING.

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