de Jong S et al. BMC Genomics 2010, 11:20 http://www.biomedcentral.com/1471-2164/11/20 addition, the correlation between the eigengenes for the Red, Pink and Magenta modules with expression values of all probes (i.e. ‘module membership’) detected on the expression arrays are given in Additional File 3. Preservation of modules To assess the preservation of the modules within each strain and brain region, multiple post-hoc analyses were performed. Samples were either separated by strain (containing amygdalar and hippocampus samples, n = 17 A/J samples, n = 18 C57BL/6J samples) or brain region (containing samples from both A/J and C57BL/6J origin, n = 17 amygdalar samples, n = 18 hippocampal samples). Networks of co-expressed genes were con- structed for these different groups using the color cod- ing from the previous module definition (using all samples from both strains). To assess the existence of the brain region specific modules in separate strains, networks of co-expressed genes were constructed for each strain separately (using both amygdalar and hippocampus samples per strain) and using the color code of the previous module defini- tion (using all samples of both strains). Modules are preserved when genes with the same color continue to cluster together based on their topological measure in the separate networks. Visual inspection of the Page 5 of 14 hierarchical clustering trees shows that this is the case for the Red and Pink modules, but not for the Magenta module (see Additional File 4). The preservation of module eigengene significance of the Red and Pink modules was used to validate these gene networks as enriched with genes differentially expressed between amygdala and hippocampus independent of origin of strain. The module eigengene correlation for the Red module was significant in both the A/J (r = 0.99, p = 2.4e-16) and C57BL/6J (r = 0.99, p = 5.4e-14) networks. The Pink module also remained significant on compar- ing amygdala and hippocampus in A/J and C57BL/6J (r = 0.88, p = 7.7e-05 and r = 0.82, p = 3.8e-05). To assess the preservation of the Red and Pink modules, we used a connectivity-based module preservation mea- sure described in [8,25,35]. Specifically, for a given module, this preservation measure is defined as the correlation of the intramodular connectivity between the two strains. Thus, the higher the value of the module preservation measure, the better preserved is the module structure (its connectivity pattern) between the two strains. For the Pink and Red modules, we found a highly significant module preservation measure (r = 0.53 p < 10e-03) and (r = 0.51 (p < 10e-03), respectively, which shows that these modules are highly preserved between the two strains. Figure 3 Gene expression heat map for significant modules. The rows correspond to genes and the columns to samples, with samples groups indicated at the top. Genes colored green are under-expressed, while red indicates over-expression. Expression in the Magenta module (top panel) is lower in A/J compared to C57BL/6J for almost all probes. Both up- and down-regulated probes compose the Pink (middle panel) and Red (bottom panel) modules when comparing amygdala and hippocampus.