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Centrality threshold based hills: as a natural choice, hills may be identified as the connected components of the community landscape above a given threshold.
Betweenness centrality threshold is set in the same way as degree threshold.
In addition, the number of neighbors with significantly higher closeness centrality (threshold 0.2) is higher in the AICR network compared with random network (Additional file 5: Figure S2).
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The centrality threshold-based hill determination approach is appropriate whenever the goal of the analysis is to find modules without overlapping regions.
For the hill determination on the community landscape we presented two main approaches (for other possibilities see Section V. in the Electronic Supplementary Material S1): the centrality threshold-based hill determination and the local maxima based hill determination approaches.
As the centrality threshold-based approach is very general, most of the former methods yielding non-overlapping modules can be interpreted in the ModuLand method family as the application of the threshold-based hill determination method over an appropriate community landscape.
However, the plots also indicate the enormous sensitivity of the degree centrality to the threshold level, as significant differences in the centrality values are observed between different thresholds.
We then calculate the normalized STD of the eigenvalue centrality for different thresholds, ranging from 0 to 0.95 correlations.
95% ile threshold of centrality measures for comparisons of other methods.
By changing the criteria for degree, betweenness, eigenvector, or leverage centrality over a range of thresholds, the metrics were compared in terms of accuracy in identifying network hubs with results determined by functional cartography described above.
Using different thresholds for betweenness centrality, degree and PCC, we obtained different numbers of drug-gene pairs.
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