Similarity matrices show the relative similarity between two things. This similarity matrix shows the similarities between genes. The same list of genes is across the x and the y axis of the graph. The relative similarity is shown by the lightness or darkness of the color that corresponds to two different genes on the graph. The location that corresponds to the same gene is shown as a white box with a black line through it.
http://www.biomedcentral.com/1471-2164/8/353/figure/F5?highres=y
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