Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies

Table 1

Description of network properties for pathway topology of pathways used in simulations, compared to the properties of the two effect pathways hsa04020 and hsa04022. Nodes equal the number of included genes, links give the number of interactions, inhibition links the count of interactions of inhibiting type, the average degree of a node is the mean number of adjacent edges, density is the ratio between numbers of existing links and possible links, diameter denotes the distance to the farthest node in the graph, transitivity (also called cluster coefficient) calculates the probability of adjacent vertices of a vertex being connected, and signed transitivity considers the type of interaction in this calculation.

	Min	Mean	Median	Max	hsa04020	hsa04022
Nodes	29.00	103.60	86.5	398.00	180.00	167.00
Links	1.00	197.81	87.5	1493.00	297.00	372.00
Inhibition links	0.00	27.08	10.50	148.00	7.00	67.00
Average degree	0.07	3.18	2.36	15.62	3.30	4.46
Density	0.00	0.03	0.03	0.16	0.02	0.03
Inhibition degree	0.00	0.52	0.24	2.62	0.08	0.80
Diameter	1.00	7.36	7.00	18.00	6.00	7.00
Transitivity	0.00	0.02	0.00	0.14	0.00	0.03
Signed transitivity		0.01	0.00	0.10	0.00	0.03