Matrix displays. (A) Unclustered expression matrix display. Each row corresponds to a gene, and each column to a biological sample. The color of the (i, j) cell in the matrix indicates the expression level of the ith gene in the jth sample. Green represents below-average expression level; Red represents above-average expression level (color scheme can be adjusted by the user). (B) The same dataset as in A, with genes ordered according to a clustering solution. Horizontal white lines separate the different clusters. (C) Unclustered similarity matrix display. The color of the (i, j) cell in the matrix represents the similarity between the expression patterns of the ith and the jth genes over all the samples (hence the matrix is symmetric). Red represents high similarity, and green represents low similarity. (D) Same as in C, with genes ordered on both axes according to a clustering solution. Clusters appear as distinct red blocks along the matrix diagonal, and similar clusters are manifested by off-diagonal reddish blocks.
Shamir et al. BMC Bioinformatics 2005 6:232 doi:10.1186/1471-2105-6-232