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Figure 6 | BMC Systems Biology

Figure 6

From: Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease

Figure 6

Caudate nucleus samples exhibit significant segregation by diagnosis in gene co-expression module M8C (salmon). Analysis of caudate nucleus (CN) sample network properties for genes comprising the CN salmon co-expression module M8C [21]. (A) Average linkage hierarchical clustering of samples using 1 – ISA (intersample adjacency) as a dissimilarity measure. Colors denote control (CTRL) subjects (darkgreen; n = 31) and Huntington’s disease (HD) subjects with varying grades of disease severity: HD grade 0 (black; n = 2), HD grade 1 (red; n = 11), HD grade 2 (turquoise; n = 16), HD grade 3 (blue; n = 5), and HD grade 4 (brown; n = 1). Standardized sample connectivities ( Z.K; B) and standardized sample clustering coefficients ( Z.C; C). (D) HD and CTRL samples segregated into two distinct groups when depicted in terms of Z.K and Z.C (linear least squares regression line in black [CTRL] and red [HD]). (E) Multivariate linear regression revealed a highly significant effect of diagnosis (Dx) on the salmon module eigengene. Blue line: P = .05; red line: Bonferroni correction for multiple comparisons. (F) Heat map of expression levels for genes comprising the salmon co-expression module M8C. Rows correspond to probe sets (genes) and columns correspond to samples. Green = low expression; red = high expression. Samples in (B–D, F) are colored as in (A).

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