Similarly to the analyses performed for the comethylation network here I also analysed chromosomal enrichment (no pvalues have been calculated yet) and clustering of genes that belong to one module within a chromosome. It appears that out of 66 identified modules (including the grey module) 52 modules have at least 50% of the genes coming from a single chromosome. Here are just a few examples of these modules: 
And a few examples of modules that come from a number of different chromosomes:
A pdf file that shows histograms of frequency of genes from chromosome within each module can be found in thunk.
Next I looked at the clustering of genes within a chromosome for those modules that have at least 50% of there genes coming from the same chromosome. I binned all genes from a particular chromosome in 50 kb genes and counted the number of genes within each bin. Next, I also binned the genes within that chromosome for each module for which that chromosome contributed the most number of genes. Here are a few examples:
This clustering of genes within a specific locus of a chromosome, even chromosome arm suggests that DNA amplification or deletions could cause coexpression module formation.