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Figure 6 | Genome Biology

Figure 6

From: High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

Figure 6

Case study: RMs in nitrogen depletion EPM 2. (a) EPM 2 of the nitrogen depletion condition is represented by two matrices. The upper matrix represents the overlap between the target genes of the regulators in the EPM, and blue boxes represent the RMs. The lower matrix represents the enrichment of the target genes per regulator in the GO 'biological process' categories. For simplicity, only selected categories are shown. A more detailed explanation is presented in Additional data file 4, and the complete matrices with all significantly enriched categories (p value < 0.01) are presented in Additional data file 11. In the graph, yellow ellipses indicate the RMs. Blue lines represent a significant overlap (OL ≥ 0.5) between the target genes of the two transcription factors at nodes, and green lines represent synergistic links identified by the hypergeometric test for transcription factor pairs (see Materials and methods). The detailed information about other EPMs and RMs is available in Additional data file 11. (b) Potential regulatory scheme among the regulators in the nitrogen depletion EPM 2. Solid arrows indicate the regulator-target gene relationship from the prediction under the nitrogen depletion condition, and dotted arrows indicate the transcription factor binding information from ChIP-chip data. Gat1 is included for completion of the hierarchy, although it is not among the predicted regulators of the nitrogen depletion EPM 2.

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