de Jong S et al. BMC Genomics 2010, 11:20 http://www.biomedcentral.com/1471-2164/11/20 Page 4 of 14 Figure 2 Module eigengene values can separate samples based on mouse strain or brain region. The module eigengene is a single representative expression profile for each sample, based on the first principal component of that module. The box plots show that the Magenta eigengene values separate samples perfectly into an A/J and C57BL/6J group (b) but not brain region (a). The Red module eigengenes creates groups of amygdala and hippocampus samples (c), but does not separate between strains (d). The Pink module eigengene differentiates between brain regions as well, but to a lesser extent (e and f). Figure 2a-f and Additional File 1 show the eigengene expression values of the Magenta, Red and Pink mod- ules. The eigengene comparison showed that the Magenta module completely separates the inbred mouse strains, while the Pink and Red modules distinguish the amygdala and hippocampus independent of strain origin. The Red module is most informative in distinguishing the brain regions amygdala and hippocampus. A heat map of the Magenta module revealed a distinct pattern of overall decreased expression levels in A/J compared to C57BL/6J (Figure 3). The heat map of the Pink and Red modules showed a more random distribu- tion of increased and decreased gene expression levels on comparing amygdala and hippocampus. The full data set with the Magenta, Red and Pink module gene con- tent is available online (see Additional File 2). In