Moreover, considering specificity of compounds may result in more biologically meaningful pathways, since metabolic pathways seem to represent paths through the least "promiscuous" compounds [ 18].
Then we tested whether our biologically derived warfarin metabolic pathway was empirically significant through 100 permutations of random biological pathways using the Cooper et al. data.
First, a parameter to control the minimum number of genes can be set to remove the numerous small and biologically uninteresting pathways from the pathway set.
However, if biologically important pathways cross multiple predefined pathways (or gene sets) they might not be picked up by these approaches, which do not allow flexibility in pathway definitions.
To this aim we used EuGene to generate "Pathway Signatures", recapitulating the biologically meaningful pathways related to some clinical/biological variable of interest, and used them in an analysis workflow to compare different microarray experiments.
Of the biologically relevant pathways observed, the signal transduction pathway contained 147 differentially regulated genes, the most of any pathway (Table 2).
In addition to identifying well-known drivers, CHASM identified potential drivers not previously associated with endometrial cancer, in biologically relevant pathways: viz MTOR in the PI3K pathway and GSK-3B in the Wnt signalling pathway).
Differentially expressed genes were corresponding to different biologically relevant pathways including metabolic and oxidative stress pathways.
However, MSEA can automatically direct the investigator to biologically important pathways, and remove manual searching of pathway databases.
Pathway ranking has been shown to extract biologically meaningful pathways in small metabolic sub-networks (Takigawa and Mamitsuka, 2008).
