Table 1 Formulation of the different questions asked by the different genesets analysis methods

Q₀

Which known genesets are associated with different expression profiles under the two conditions compared?

Q_comp

Which geneset definitions are associated with the biggest difference in expression profiles observed under each condition?

Q_self

Which genesets are associated with diverging expression profiles between conditions compared with random definitions of phenotype?

Q_cor

Which genesets are defined by members associated with correlated expression changes?

Q_uni

Which genesets are associated with an increase or decrease of all member expression values?

Q_bidir

Which genesets are defined by differentially expressed genes, regardless of the direction of the regulation?

Q_int

Which genesets are associated with variable individual expression changes?

Q_u^c

Which unidirectional groups have members that are associated with a correlated answer?