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Figure 4 | BMC Systems Biology

Figure 4

From: Extracting expression modules from perturbational gene expression compendia

Figure 4

Mating module 77. A module enriched in pheromone response genes. The colors of individual spots reflect the expression ratios (experiment vs. control, blue = upregulated, yellow = downregulated, white = missing value). The module is split in leafs in both dimensions based on average linkage clustering using a cosθ threshold of 0.65. In order not to crowd the figure, leafs of size < 3 are grouped in a single leaf beyond the red line (rightmost leaf and bottom leaf). Transcription factors are highlighted in yellow in the gene list if there is ChIP data available for them, while other regulators are highlighted in red. To the right of the expression matrix is a column indicating the module's seed genes (red). Further to the right is a matrix depicting the presence of enriched TF binding sites (yellow) and/or significant co- or antiexpression links with potential regulators (green and red, respectively; the hue is proportional to the p-value of the link; in case of overlap with an enriched binding site, the field is colored dark green or dark red). The expression profiles of these regulators are depicted on top of the module's expression matrix. Note that regulators that are part of the module are not repeated on top unless they also exhibit significant binding site enrichment. To the far right are matrices depicting the genes' membership of enriched GO categories (orange) and membership of other modules (blue). The black and magenta arcs represent protein and genetic interactions, respectively. The arrow indicates the tec1 Δ experiment (see main text).

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