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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