Hierarchical cluster analysis showing the genetic architecture of gene expression in skeletal muscle. Unsupervised hierarchical cluster dendrogram of gene expression was undertaken using 40 skeletal muscle samples derived from the progeny of six sires characterised as having high or low EBVs for the trait EMD (Eye Muscle Depth). Clustering was undertaken by using GeneSpring GX software (Agilent Technologies) with selection for "condition tree" and "gene tree" with "Standard Correlation". Rows represent individual animals while columns represent genes. Different colours in the heat map represent gradients of gene expression levels: red, higher expression; blue, lower expression; yellow, no difference in gene expression. The branch lengths indicate the correlation with which samples were joined, with longer branches indicating a lower correlation. Individual genes could not be resolved at this magnification. (a) Branch length coloured for sire group. Sire group I, light blue; II, red; III, brown; IV, yellow; V, purple; VI, dark blue (the colours do not correspond with any of those used in subsequent network analyses). (b) Branch length coloured for sire EBV for EMD: red, high EBV group; yellow, low EBV group.