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How do I interpret the cluster images?
Hierarchical clustering arranges genes according to their similarity in expression profiles across all of the array experiments, such that genes with similar expression patterns are "clustered" together. The gene expression data are displayed in tabular format in which each row of colored boxes corresponds to the variation in transcript level for each gene, and each column represents the variation in transcript levels of every gene in a given mRNA sample, as measured on one array. The variation in transcript abundance is represented by a color scale in which shades of red represent increases and shades of green decreases in transcript abundance, relative to the unstressed reference sample, and the saturation of the color corresponds to the magnitude of change. A black color indicates an undetectable change in transcript abundance, and a grey color indicates missing data.

How is the similarity between two genes determined?
The similarity of two genes in expression space is determined by calculating a distance measure across all experimental values. For this we are using the Pearson correlation coefficient.

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