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).
de Jong et al. BMC Genomics 2010 11:20 doi:10.1186/1471-2164-11-20