Identifying cell cycle transcription factors (TFs) is important for understanding the transcriptional regulation of the cell cycle process which controls the growth and development of all organisms. Existing computational approaches for identifying cell cycle TFs are mainly based on methods with a fixed selection criterion. That is, the same criterion was applied to each TF to determine whether it is a cell cycle TF or not. Since the characteristic of each TF may be quite different, it is not suitable to use a fixed selection criterion in identifying cell cycle TFs. Instead of using a fixed selection criterion, we propose a method with variable selection criteria to identify cell cycle TFs in yeast by integrating the ChIP-chip and cell cycle gene expression data. Our method is shown to outperform five existing methods which used the same ChIP-chip dataset as we did. Fifteen cell cycle TFs were identified by our approach, 12 of which are known cell cycle TFs, while the remaining three (Hap4, Reb1 and Tye7) are novel cell cycle TFs. The biological significance of our predictions is shown by four lines of indirect evidence derived from the protein-protein interaction data, TF mutant data, ChIP-chip data and the results of the previous computational studies.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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Evidence ID | Analyze ID | File | Description |
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