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Table 2 Properties of gene interaction networks and modules derived from the networks under different similarity measures. All values are for the one-square matrix transformation method. See Methods and Discussion for detailed discussion, Figs. 3 and 4 for visual representation of the data, and supplementary online materials for generally similar results obtained under the two-square transformation

From: Measuring similarity between gene interaction profiles

Similarity measure Braun-Blanquet Maryland Bridge Ochiai Pearson
Similarity threshold applied to retain ~ 20,000 edges in the network 0.16 0.18 0.20 0.15
Nodes (genes) in the network / nodes (genes) in the giant connected component 3427 / 3303 3610 / 3587 3385 / 3321 4038 / 3956
Edges in the network / edges in the giant connected component 20,020 / 19,943 20,065 / 20,052 20,067 / 20,032 20,016 / 19,967
Unique genes in modules / percentage of all genes in respective giant connected component 2072 / 62.7 725 / 20.2 1519 / 45.7 3072 / 77.6
Number of modules / unique genes per module 682 / 3.04 408 / 1.78 516 / 2.94 1446 / 2.12
Biological Homogeneity Index 0.12 0.27 0.16 0.33
Percentage of uncharacterized genes / p-value / clusters with uncharacterized genes 36 / 10−38 / 38 17 / 10−11 / 2 36 / 10− 22 / 30 26 / 10− 3 / 35
Annotated modules of Type 1 / Type 2 36 / 409 64 / 119 48 / 309 279 / 568