Because gene coexpression patterns may reflect multiple sources of variation, comparisons between networks provide an important validation. Although a majority of gene coexpression modules identified in cerebral cortex were present in both CTX and CTX_95, and many of these modules were also present in CTX_ILMN, it is important to consider the potential explanations for observed discrepancies among the cortical networks. Some discrepancies probably resulted from differences in platform and probe set design, as well as the representation of genes on the microarrays, whereas others may have resulted from biological differences between individuals and cortical areas. Although we found few modules of coexpressed genes driven by specific cortical areas (for example, M17B and M23), we cannot exclude the possibility that the batch normalization method applied here may have obscured area-specific gene expression patterns. However, our results are consistent with previous microarray studies that have identified few differences in gene expression between association areas in adult human cortex2,3. Future studies of gene coexpression relationships in discrete cortical areas may shed light on this issue.
