Figure 4.

Permutation test results for showing that the number of genes in consensus modules is highly significant. Here we use the brain and muscle tissues of female mice. The size of a consensus module depends on the height cut-off used for cutting branches off the dendrogram. Thus, the number of genes in a consensus module (y-axis) depends on the height cut-off (x-axis). The red horizontal lines represent the observed number of genes in consensus modules for the original (unpermuted) data set. The boxplots (black) summarize the number of genes assigned to consensus modules after the gene list has been permuted between the two data set (1000 random permutations). For height cut-offs less than 0.99, the observed number of consensus genes is highly significant (p = 0.001).

Langfelder and Horvath BMC Systems Biology 2007 1:54   doi:10.1186/1752-0509-1-54
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