Figure 4.

Specific patterns of gene-expression changes are associated with templates. Conserved word-pair templates are shown with significant associations with gene-expression changes in (a) multiple environmental stress conditions or (b) distinct subsets of environmental conditions. The P × C matrix of K-S p-values was hierarchically clustered by rows and visualized with TreeView [52]. Each row corresponds to a conserved word-pair template, and each column represents a single gene-expression experiment. The experimental conditions are indicated by the color bar above each panel, according to the key. The value in each cell corresponds to the K-S p-value of gene-expression changes in each condition (column) for a group of genes that contain the conserved word-pair template (row) in their TCRs. Orange denotes a K-S p-value below the FDR critical value of 0.001 for multiple testing, while gray represents values that were not significant. Word pairs that failed to meet a FDR critical value of 0.001 for multiple testing in five or more experiments are not shown. Some of the most significant conserved word-pair associations are labeled and annotated in Tables 1 and 2.