Table 2

Simulation conditions for comparing various methods for pathway enrichment

Pattern number

Network

Correlated set (Σ)

Target set (Φ)


1

Linear

{g1,..., g9}

2

Linear

UL

3

ErbbSignaling

4

ErbbSignaling

UE

5

Linear

Ø


Different correlation patterns (1-5) considered for the generation of simulated data along with the underlying networks, the set of correlated genes, Σ, and the set of genes that are the targets of the treatment, Φ. UL denotes a uniformly randomly drawn set of nine genes drawn from the set of genes associated with the pathway displayed in Figure 1a. V41L denotes a set of 41 randomly drawn genes from the set of 470 genes not associated with the pathway displayed in Figure 1a. UE denotes a uniformly randomly drawn set of seven genes drawn from the set of genes associated with the pathway displayed in Figure 1b. V3E denotes a set of three randomly drawn genes from the set of 413 genes not associated with the pathway displayed in Figure 1b. Ø denotes the empty set. The symbol ∪ denotes the set union operation.

Thomas et al. Genome Biology 2009 10:R44   doi:10.1186/gb-2009-10-4-r44

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