A human functional protein interaction network and its application to cancer data analysis

Table 6 Average shortest distance for GBM clusters

Data set	Cancer genes	Random permutation (P-value)	Degree-based permutation (P-value)
TCGA	2.29	3.83 (< 0.001)	2.86 (<0.001)
Parsons	2.76	3.82 (< 0.001)	3.32 (<0.001)

The values in the 'Cancer genes' column are from the cancer clusters, while those in the two permutation columns are from permutation tests. Random permutation is done via randomly picking up the same number of genes from the biggest connected graph component as for the cancer genes, and degree-based permutation is done by picking up genes from different bins based on the degree distributions of cancer genes. The gene bins are dynamically generated based on the sorted list of degrees from the cancer genes.

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