expression distributions of the two patient groups                                                                                          None                             Single gene                             mRNA expression of the gene
  Lee [*et al.*]{}[@Lee2008]         L,[*Lee*]{}       Calculates for each pathway a set of genes with high t-statistic between the averaged gene expression and the two patient groups                                                MsigDB, KEGG                     Subset of genes in a pathway            Averaged mRNA expression of genes in set
  Chuang [*et al.*]{}[@Chuang2007]   C, [*Chuang*]{}   Calculates subnetworks with high mutual information between the averaged gene expression of the genes in the subnetworks and the class labels of the two patient groups         KEGG, HPRD, I2D, NetC            Genes in a subnetwork                   Averaged mRNA expression of the genes in the network
  Taylor [*et al.*]{}[@Taylor2009]   T, [*Taylor*]{}   Finds hub proteins that, given the two patient groups, show different Pearson correlation of the mRNA expression between the hub proteins and all of their direct interactors   KEGG, HPRD, I2D, NetC            Edge between a hub and its interactor   Difference of mRNA expression of hub and its interactors (edge weights)

  : Overview of evaluated feature extraction methods.

As secondary data sources we used the KEGG database [@Kanehisa2010] and the C2 data set of the MsigDB [@Subramanian2005], as PPI data we used the information from KEGG, HPRD [@Prasad2009] and the OPHID/I2D databases [@Brown2005]. In 