PMC

Gene expression signature comparisons. (a) Visual display of the 3 h reference cold signature and identification of similarly ranked genes, as denoted by adjacent black and gray lines, with the query cold signature. The rank, identification, and annotation for the 10 most similarly ranked up- and down-regulated genes are described. (b) Display of the 6 h UV-B reference signature and identification of similarly ranked genes with UV-B query signature. The rank, identification, and annotation for the 10 most similarly ranked up- and down-regulated genes are described.

Gene expression signature comparisons. (a) Visual display of the 3 h reference drought signature and identification of similarly ranked genes, as denoted by black lines, with the singular query drought signature. The Rank, identification, and annotation for the 10 most similarly ranked up and down genes are described. (b) Display of the 3 h drought reference signature and identification of similarly ranked genes with simultaneously imposed heat and drought query signature. The Rank, identification, and annotation for the 10 most similarly ranked up and down genes are described.

Gene expression signature comparisons. (a) Visual display of the 3 h reference heat signature and identification of similarly ranked genes, as denoted by black lines, with the singular query heat signature. The Rank, identification, and annotation for the 10 most similarly ranked up and down genes are described. (b) Display of the 3 h heat reference signature and identification of similarly ranked genes with simultaneously imposed heat and drought query signature. The Rank, identification, and annotation for the 10 most similarly ranked up and down genes are described.

Relationship between expression abundance and module association. (a) Patterning of gene expression architecture relative to time of osmotic treatment. The patterns are structured according to expression abundance and the corresponding gene module. (b) Relationship between Chi square enrichment (X²) of differentially expressed genes and time of osmotic stress treatment. (c) Visual patterning of gene expression architecture relative to 3 h of drought, osmotic, salt, UV-B, heat, and cold treatments.

Visual representation of the AtGenExpress abiotic gene coexpression network. (a) A dendrogram of the 4000 most connected genes grouped into six distinct coexpression modules. The red line indicates the height at which the tree was cut to produce the distinct gene clusters (modules) as denoted by the color bar. (b) Multi-dimensional scaling plot of the gene coexpression network. Each circle represents a single gene and the color of the circle corresponds to module designation. The distance between circles is a function of the topological overlap and provides a visual representation of gene and module relationships within the network.

Relationship between modules and plant stress phenotype. Red-green heat maps depict mean differential gene expression between control and treatment conditions (x-axis) for all genes specific to the turquoise (A), yellow (B), brown (C), blue (D), green (E), and red (F) modules. Each horizontal line within a heat map shows the expression values (in terms of color) for the same gene across treatments. Red is increased expression, black is neutral, and green is decreased expression in comparison to the control treatment. The black triangles denote the direction of increasing treatment exposure. The corresponding bar plots are the eigengene values, first principle component, as determined from singular value composition for each module. Each bar is the average of two eigengene values.