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Figure 1 | BMC Systems Biology

Figure 1

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

Figure 1

Network concepts provide a natural framework for describing relationships among samples in high-dimensional biological datasets. A motivational example. (A) Dendrogram produced by average linkage hierarchical clustering using 1 – ISA (intersample adjacency) for a subset of samples (prefrontal cortex [BA9] of CTRL subjects) from ref. [14]. (B) Dendrogram produced by average linkage hierarchical clustering using 1 – ISA for another subset of samples (cerebellum [CB] of CTRL subjects) from ref. [14]. (C) Standardized sample connectivities (Z.K) provide a different view of the BA9 CTRL samples. BA9_91_C (red) exhibited significantly lower connectivity than the other samples in this group, consistent with the dendrogram (A). (D) Standardized sample connectivities for the CB CTRL samples. Three samples (CB_80_C, CB_H123_C, and CB_67_C, in red) had Z.K values that were significantly lower than the others. Note that CB_67_C had much lower connectivity than CB_H110_C (blue), yet these two samples were indistinguishable in the dendrogram above (B). Black horizontal lines in (C) and (D) correspond to an optional Z.K threshold (here −2) for outlier removal; CTRL = control.

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