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Figure 1 | BMC Genomics

Figure 1

From: Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression

Figure 1

Comparison of chromatin immunoprecipitation and transcriptome data at low and high Leu3 activity. (A) Venn diagram showing the number of genes bound and/or regulated at low concentrations. (B) Association of Leu3 binding sites with the indicated subset of genes defined as bound and/or regulated at low concentrations. All genes were scored for predicted Leu3 binding potential using GOMER [8], and ranked according to this score. Genes in the indicated subset were compared to all other genes in the genome using a receiver operator characteristic curve (ROC), and the value of the area under the curve is shown in this histogram. The histogram starts at a value of 0.5 because that is the value expected by chance. A value of 1.0 would indicate that the predicted binding potential scores perfectly discriminate the experimentally defined subset of genes from all others. (C) The fraction of genes in each low concentration subset that have Gene Ontology process annotations that are significantly enriched (P ≤ 1e-6). Gene ontology analyses were performed using the Saccharomyces Genome Database web site [21]. (D–F) These panels are analogous to panels A–C except that the genes were defined based on experiments using constitutively active protein expressed at higher-than-endogenous levels.

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