UniBind 2021 permissive Track Settings
 
UniBind 2021 track for permissive Caenorhabditis elegans direct TF-DNA interactions

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Data last updated at UCSC: 2021-04-26 07:23:26

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.
The UniBind database hosts the complete set of TFBS predictions, as well as the prediction model itself, and cis-regulatory modules (CRMs) derived from these direct TF-DNA interactions. All the data is publicly available. For further details, please refer to the associated publications:

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:
ATF-7
BLMP-1
CEBP-1
CEH-22
CEH-28
CEH-48
CHE-1
DAF-12
DAF-16
DPY-27
DSC-1
EFL-1
ELT-2
ELT-3
EOR-1
FKH-2
FOS-1
HLH-1
HLH-30
LIN-14
LIN-54
MAB-5
NHR-6
PHA-4
PQM-1
SKN-1
SNPC-4
UNC-30
UNC-62
UNC-86
ZIP-8

Methods

The entire collection of ChIP-seq data sets was uniformly processed in ReMap and GTRD up to ChIP-seq peak calling. The entire collection of ChIP-seq peaks is also available in the ReMap and GTRD databases, respectively. 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://unibind2021.uio.no.

Reference

If you use UniBind or ChIP-eat in your work, please cite:

R. Riudavets Puig, P. Boddie, A. Khan, J.A. Castro Mondragon, A. Mathelier,
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BioRxiv (2020) https://doi.org/10.1101/2020.11.17.384578.

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: