Figure 6.

Network topology of ranked interactions. (A) We reconstructed the corresponding top-ranked protein-protein interactions (PPIs) networks using both interaction detection based on shuffling (IDBOS) ranking and frequency of occurrence ranking. The columns of 4,425, 6,561, and 13,554 top-ranked interactions corresponds to selecting PPIs with ≥ 4, ≥ 3, and ≥ 2 reported occurrences, respectively. These interactions were distributed among roughly twice as many proteins using IDBOS ranking than in occurrence ranking. (B) The degree distribution for each selected PPI network was analyzed and compared to the distribution of all aggregated interactions (All). The higher-ranked PPI data sets were associated with fewer proteins that had a large number of interacting partners (hubs). As visualized in (A), the top-ranked networks were instead characterized by more evenly distributed interactions in a loosely interconnected network.

Yu et al. BMC Bioinformatics 2012 13:79   doi:10.1186/1471-2105-13-79
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