Grid-layout visualization method in the microarray data analysis interactive graphics toolkit

The expression levels of thousands of genes in different tissues or cells in different conditions can be detected all at one time by DNA microarray technology. A new, grid-layout method for the visualization results of hierarchical cluster analysis of DNA microarray data is proposed and incorporated in the microarray interactive graphics toolkit (MIGT). The grid-layout consists of a set of regular, two-dimensional grid units. Each unit represents a cluster or a group of gene clusters. The units are connected to adjacent ones by the neighborhood relation of the clusters in a hierarchical tree. Nodes lying near each other in the hierarchical tree are mapped onto nearby grid-layout units. The number of units may vary on a scale from a few dozen up to several thousands, depending on the number of the nodes in a hierarchical tree. Different colors are assigned to the units with RGB value according to the coordinates of the units, and the inter-distances, which are the distances between clusters in a hierarchical tree, and the intra-distances, which are the distances between genes within one cluster. The closer the inter-distances, the more similar the color of the units are, the smaller the intra-distances, the warmer the color of the unit is.