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"