UniBind Track Settings
 
UniBind: A map of direct TF-DNA interactions in the human genome

Display mode:   
View table schema
Data last updated at UCSC: 2019-04-23 06:56:04

UniBind: A map of direct TF-DNA interactions in the human genome

Description

We provide here the track hub that corresponds to the map of direct TF-DNA interactions (aka TFBSs) stored in the UniBind database.
UniBind is a comprehensive map of direct transcription factor (TF) - DNA interactions in the human genome. These interactions were obtained by uniformly processing ~2,000 public ChIP-seq data sets, from raw reads to high confidence TF binding site predictions, using the ChIP-eat software. The uniform processing, up to ChIP-seq peaks calling was performed by ReMap and the entire collection of ChIP-seq peaks is also available in the ReMap database. ChIP-eat used the MACS2 peak caller to identify ChIP-seq peaks on the hg38 version of the human genome. 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. The UniBind database hosts the complete set of TFBS predictions for each prediction model, as well as the models themselves, the original ChIP-seq peaks, and cis-regulatory modules derived from these direct TF-DNA interactions. All the data is publicly available. For further details, please refer to the associated publication: (DOI: 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://unibind.uio.no.


Display Conventions and Configuration

  • Each transcription factor follow a specific RGB color.
  • 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 identifier>.<cell type/tissue>_<condition>.<TF name>.<JASPAR ID>.<JASPAR version>.<TF binding model>

Methods

The entire collection of ChIP-seq data sets was uniformly processed in ReMap up to ChIP-seq peak calling. The entire collection of ChIP-seq peaks is also available in the ReMap database. These peaks served as input for the ChIP-eat data processing pipeline. The complete pipeline is designed to uniformly process ChIP-seq data sets, from raw reads to the identification of direct TF-DNA binding events, and it was implemented in the ChIP-eat software with source code freely available at https://bitbucket.org/CBGR/chip-eat/. Only the ChIP-seq datasets for which a TF binding profile for the targeted TF was available in JASPAR were used for TFBS predictions. The enrichment zone containing high confidence direct TF-DNA interactions was automatically defined for each data set using an entropy-based algorithm. The diagram below illustrates the processing steps.


ChIP-eat workflow



Data Availability

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

Reference

If you use UniBind or ChIP-eat in your work, please cite:
M. Gheorghe, G.K. Sandve, A. Khan, J. Cheneby, B. Ballester, and A. Mathelier,
A map of direct TF-DNA interactions in the human genome. Nucleic Acids Research (2019) gky1210 https://doi.org/10.1093/nar/gky1210.

Contact

If you have questions or comments, please write to: