Accompanying data for 10.5281/zenodo.8327373, Codebook HT-SELEX, subsampled reads. Update 2025: finalized files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

Accompanying data for 10.5281/zenodo.8327373, Codebook HT-SELEX, subsampled reads. Update 2025: finalized files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the binding specificities of human transcription factors, see Vorontsov et al. (bioRxiv).Motif discovery for MEX was performed with multiple software tools, and the resulting motifs were rigorously benchmarked against held-out test data. Here you can find detailed benchmarking results, complete motif sets, and the benchmarking-ready preprocessed experimental data. Further details are provided in README.Note: There are two extra accompanying Zenodo datasets, namely,doi:10.5281/zenodo.8327477 (MEX HT-SELEX data) and doi:10.5281/zenodo.8327970 (MEX GHT-SELEX data). Update 2025: replaced files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.Note: PBM and SMS datasets were not affected and the respective files remain the same as in the previous upload.This repository now also provides the set of reference artifact motifs used to filter the MEX results in a variety of commonly accepted formats (TRANSFAC, MEME, JASPAR, plain text).In the last version, we have resolved remaning minor issues with motif metadata and metrics, and included top1-top20 motifs and logos, according to the MEX rankings.

This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the binding specificities of human transcription factors, see Vorontsov et al. (bioRxiv).Motif discovery for MEX was performed with multiple software tools, and the resulting motifs were rigorously benchmarked against held-out test data. Here you can find detailed benchmarking results, complete motif sets, and the benchmarking-ready preprocessed experimental data. Further details are provided in README.Note: There are two extra accompanying Zenodo datasets, namely,doi:10.5281/zenodo.8327477 (MEX HT-SELEX data) and doi:10.5281/zenodo.8327970 (MEX GHT-SELEX data). Update 2025: replaced files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.Note: PBM and SMS datasets were not affected and the respective files remain the same as in the previous upload.This repository now also provides the set of reference artifact motifs used to filter the MEX results in a variety of commonly accepted formats (TRANSFAC, MEME, JASPAR, plain text).In the last version, we have resolved remaning minor issues with motif metadata and metrics, and included top1-top20 motifs and logos, according to the MEX rankings.

This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the binding specificities of human transcription factors, see Vorontsov et al. (bioRxiv).Motif discovery for MEX was performed with multiple software tools, and the resulting motifs were rigorously benchmarked against held-out test data. Here you can find detailed benchmarking results, complete motif sets, and the benchmarking-ready preprocessed experimental data. Further details are provided in README.*The version update resolves minor file naming issues in the original upload. The files contents remain the same.Note: There are two extra accompanying Zenodo datasets, namely,doi:10.5281/zenodo.8327477 (MEX HT-SELEX data) and doi:10.5281/zenodo.8327970 (MEX GHT-SELEX data). Update 2025: replaced files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.Note: PBM and SMS datasets were not affected and the respective files remain the same as in the previous upload.This repository now also provides the set of reference artifact motifs used to filter the MEX results in a variety of commonly accepted formats (TRANSFAC, MEME, JASPAR, plain text).

Accompanying data for 10.5281/zenodo.8327373, Codebook GHT-SELEX, genomic peaks and subsampled reads. Update 2025: final update for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

Accompanying data for 10.5281/zenodo.8327373, Codebook GHT-SELEX, genomic peaks and subsampled reads. Update 2025: final update for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

Accompanying data for 10.5281/zenodo.8327373, Codebook HT-SELEX, subsampled reads. Update 2025: replaced files for TFs whose datasets were partially mislabeled in the original upload.Affected TFs: CHCHD3, CPXCR1, MYRFL, PRDM5, TIGD4, TIGD5, TTF1, ZBED5, ZBTB5, ZNF578.

This repository contains preprocessed Codebook-MEX data suitable for training and testing advanced models of transcription factor binding sites, see README for details.These data are derived from the ChIP-Seq and genomic HT-SELEX datasets of the primary MEX data release (ZENODO doi:10.5281/zenodo.8327372).  Extra:ARCHIPELAGO_models.zip: the ArChIPelago models trained on genomic HT-SELEX and ChIP-Seq data for 139 TFs. Please refer to 5_Archipelago_sav_models_loading_and_scoring.ipynb in the ArChIPelago GitHub repo (https://github.com/autosome-ru/MEX-ArChIPelago) for details on using the model for scanning arbitrary DNA sequences. * Latest update: Archipelago models and underlying data were removed for three TFs (TIGD4, TTF1, ZBED5), which were partially affected by mislabeled samples in the original upload.

This repository contains preprocessed Codebook-MEX data suitable for training and testing advanced models of transcription factor binding sites, see README for details.These data are derived from the ChIP-Seq and genomic HT-SELEX datasets of the primary MEX data release (ZENODO doi:10.5281/zenodo.8327372).  Extra:ARCHIPELAGO_models.zip: the ArChIPelago models trained on genomic HT-SELEX and ChIP-Seq data for 139 TFs. Please refer to 5_Archipelago_sav_models_loading_and_scoring.ipynb in the ArChIPelago GitHub repo (https://github.com/autosome-ru/MEX-ArChIPelago) for details on using the model for scanning arbitrary DNA sequences. * Latest update: Archipelago models and underlying data were removed for three TFs (TIGD4, TTF1, ZBED5), which were partially affected by mislabeled samples in the original upload.