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Results of four separate benchmarks of the tfbs_footprinter method and the DeepBind program. Results for PWM are included as a sub-component of tfbs_footprinter results. [https://github.com/thirtysix/TFBS_footprinting][1] 1. **strong_vs_distal** - true positives: GTRD ChIP-Seq peaks located within -900 and +200 bp relative to an Ensembl-defined protein-coding transcript, with fold-enrichment ≥50x. - true negatives: Sites 1,000 bp upstream of paired true positives. 2. **strong_vs_weak** - true positives: GTRD ChIP-Seq peaks located within -900 and +200 bp relative to an Ensembl-defined protein-coding transcript, with fold-enrichment ≥50x - true negatives: GTRD ChIP-Seq peaks located within -900 and +200 bp relative to an Ensembl-defined protein-coding transcript, with fold-enrichment ≤2x. 3. **SUPPLEMENTARY_expSite_vs_randomLocSamePromoter** - true positives: Experimentally verified functional TFBSs as annotated in the ORegAnno/Pleides/ABS datasets. - true negatives: Random locations in the same Ensembl transcript as positive the paired true positive. 4. **SUPPLEMENTARY_expSite_vs_sameTSSDistOtherPromoter** - true positives: Experimentally verified functional TFBSs as annotated in the ORegAnno/Pleides/ABS datasets - true negatives: Random locations in other Ensembl transcripts at the same distance from the TSS as the paired true positive. [1]: https://github.com/thirtysix/TFBS_footprinting "https://github.com/thirtysix/TFBS_footprinting"
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