Traditional hierarchical cluster versus ModuleFinder analysis of 374 Nuclear Genes encoding Mitochondrial Proteins (NGMPs). A) The 374 NGMPs were clustered into 16 clusters in response to 16 treatments. This analysis split genes that have related function in a subset of treatments. B) Using the same starting set of genes and treatments, but seeding the ModuleFinder with salicylic acid and rotenone treatments (indicated in red) a different grouping of genes is produced. This output contained only 51 genes, divided into 8 modules; this used a p-value cut-off of 0.1, Euclidean distance, complete linkage and a between-to-within-groups variance ratio > 4. The number to the left of the heat map indicates the cluster number that these genes belonged to in the analysis carried out in A above.