UniBind: maps of high-confidence direct TF-DNA interactions across species

Description

We provide here the track hub that corresponds to the map of permissive direct TF-DNA interactions (aka TFBSs) stored in the UniBind 2021 database.
UniBind is a comprehensive map of direct transcription factor (TF) - DNA interactions across species. These interactions were obtained by uniformly processing ~10,000 public ChIP-seq data sets using the ChIP-eat software. The uniform processing, up to ChIP-seq peaks calling was performed by ReMap and GTRD and the entire collection of ChIP-seq peaks is also available in their respective websites. An entropy-based algorithm was used to automatically delineate an enrichment zone containing direct TF-DNA interactions, supported by both strong computational evidence and strong experimental evidence. Moreover, we applied a quality control step to each set of TF-DNA interactions to identify high-quality transcription factor binding sites (TFBSs), yielding two different collections of TFBSs:

• Permissive TFBSs: a collection containing all TFBSs available in UniBind.
• Robust TFBSs: a collection containing only those TFBSs that passed the quality control. More details on the quality control metrics and the selected thresholds are described in our UniBind 2021 publication.

• UniBind 2021 publication: https://doi.org/10.1101/2020.11.17.384578).
• Original UniBind publication: https://doi.org/10.1093/nar/gky1210).

Individual BED files for specific TFs or datasets can be found and downloaded on the UniBind website at http://unibind2021.uio.no.

Display Conventions and Configuration

• A set of TFBSs derived from a specific ChIP-seq experiment with a specific TF binding profile from JASPAR is defined with a name following the format
  <GEO/ArrayExpress/ENCODE/GTRD identifier>_<cell type/tissue>-<condition>_<TF name>_<JASPAR ID>.<JASPAR version>
• Each transcription factor follow a specific RGB color according to the following table:

Methods

Data Availability

Individual BED files for specific TFs or datasets can be found and downloaded on the UniBind website at http://unibind2021.uio.no.

Reference

Contact

• Anthony Mathelier ([email protected])