As an example of the type of analysis one can perform with WGCNA, we describe a network analysis of liver expression data from female mice. The data and biological findings of this analysis have been described in [14]. Briefly, mRNA levels in female mouse livers were measured by microarrays with over 23,000 probe sets. In addition to the expression data, multiple physiological and metabolic traits were measured. For computational reasons, the original analysis presented in [14] was restricted to 3600 most connected genes, and for simplicity we will work with the same set of genes (although we note that the presented package is capable of handling all genes as well). While we do use the same data, the module detection methods are slightly different and the results are similar but not the same. The code used to perform this analysis is part of the tutorials posted on our webpage.
