Identifying binding sites of transcription factors (TFs) is a key task in deciphering transcriptional regulation. ChIP-based methods are used to survey the genomic locations of a single TF in each experiment. But methods combining DNase digestion data with TF binding specificity information could potentially be used to survey the locations of many TFs in the same experiment, provided such methods permit reasonable levels of sensitivity and specificity. Here, we present a simple such method that outperforms a leading recent method, centipede, marginally in human but dramatically in yeast (average auROC across 20 TFs increases from 74% to 94%). Our method is based on logistic regression and thus benefits from supervision, but we show that partially and completely unsupervised variants perform nearly as well. Because the number of parameters in our method is at least an order of magnitude smaller than CENTIPEDE, we dub it MILLIPEDE.
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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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