Figure 3

Expression matrix, heatmaps, GO annotations, and dendrograms. This figure shows: (a) tables of values, (b) tables of colors, (c) tables of symbols, (d) list of GO terms annotating a gene, and (e) dendrograms. In the tables of values, the names of the experimental conditions appear in the first row and usually correspond to consecutive instants in time. The first column displays the names of the genes. Each remaining cell in the table contains the expression value of a given gene in a specific condition. In the tables of colors, cells with high expression values are, by default, colored red, while the ones with low expression values are given a green color. Cells holding the mean value are colored black. The intensity of the color is set according to the actual expression value of each cell, thus generating a scale of reds and greens for all possible expression values. Cells with no expression value, that is, a missing value, are given a yellow color. Tables of symbols resemble tables of colors and are computed using a discretized version of the expression matrix. The GO terms listed as annotations of a given gene correspond to the most specific GO terms (before applying the true path rule). Dendrograms are visualized using Java TreeView [25] in a separate window. They are displayed together with the expression matrix and enable the researcher to individually select clusters, which are then displayed in a separate panel. The researcher may further change the settings of the dendrogram, search for genes or conditions within the data, compare with other hierarchical clustering results and export both the dendrogram and the gene expression matrix as vector (PS) or raster (PNG, PPM, JPG) image files.