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Figure 4 | BMC Systems Biology

Figure 4

From: Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data

Figure 4

Examples of our hypotheses that have been experimentally validated in the literature. (a) RPT4 is a knockout target of Hsf1 from Reimand et al.’s study [11]. Since the RPT4 promoter has no Hsf1 binding sites, it is hard to imagine how Hsf1 regulates RPT4. Our method identified a path Hsf1→RPN4RPT4, suggesting Hsf1 regulates RPT4 through the intermediate TF Rpn4. The identified path has been experimentally proven to exist in the yeast cells [6, 7, 2126]. (b) ETR1 is a knockout target of Stp2 from Reimand et al.’s study [11]. Since the ETR1 promoter has no Stp2 binding sites, it is hard to imagine how Stp2 regulate ETR1. Our method identified a path Stp2→ADR1ETR1, suggesting Stp2 regulates ETR1 through the intermediate TF Adr1. The identified path has been experimentally proven to exist in the yeast cells [6, 7, 23, 2729].

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