Codebook Motif Explorer Supplementary Dataset

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.