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Here (L(C subseteq X) is the set of elements (leaves) of C. Before that, cluster is defined as a particular kind of sub-graph within a dendrogram according to: Let D be a dendrogram on X.
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A subgraph C of D is a subtree (or subdendrogram) if C itself is a dendrogram on L(C).
Clustering of samples by similarity of gene expression patterns is shown as a dendrogram on the right side of the heat map, which divides the samples into two major clusters (Fig. 4, upper and lower clusters are divided by a white line).
GO-based clustering for the genes is visualised with a dendrogram on the left.
The R package pvclust version 1.3-2 (Suzuki and Shimodaira 2006) was used to build a dendrogram on the redundancy data by assessing the uncertainty in hierarchical cluster analysis via multiscale bootstrap resampling with 1,000 bootstrap replications.
Highly similar groupings of the isolates were observed when a dendrogram was built based on spoligotypes alone or on a combination of VNTR and spoligotypes, although the resolution was lower when spoligotyping was used alone (data not shown).
Jaccard's coefficient of similarity was measured and a dendrogram based on similarity coefficients was generated by using unweighted pair group method with arithmetic mean (UPGMA).
In a recent, study clonal complexes were identified in a dendrogram based on concatenated sequences derived from 102 isolates of S. mutans with cluster analysis by the unweighted pair group method using arithmetic means [35].
Prior to the gene expression analysis, the samples were paired in a dendrogram based on a comparison of the expression profiles of all the genes.
Similar patterns were also observed in a dendrogram based on HindIII ribotyping [ 10] and AFLP banding patterns [ 7, 23].
Next, the UPGMA algorithm was used to construct a dendrogram based on a matrix of pairwise allelic differences between the 62 STs of our dataset.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com