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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources

Fig. 3

Optimization by harmonic search. a The PPI network integration parameters were optimized in a way that detected modules show the highest similarity to the co-expressed modules. Normalized Mutual information (NMI) values were used as a measure to compare similarities at the detected module level and optimization were performed for 10000 iterations. b The NMI values of the best detected module set at each iteration was compared with co-functionality modules using Gene Ontology terms. Although the co-expression module set as functional modules to optimize the NMI values, still the NMI values would increase in most of the interactions when the PPI modules was compared with the co-functionality modules. c The NMI values of the best detected module set at each iteration was also compared with co-regulation modules. Likewise, NMI values would fairly increase in the majority of iterations

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