Description

This track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the JASPAR CORE collection. This open-source database contains a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.

Display Conventions and Configuration

Shaded boxes represent predicted binding sites for each of the TF profiles in the JASPAR CORE collection. The shading of the boxes indicates the p-value of the profile's match to that position (scaled between 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a p-value ≤ 10^-10). Thus, the darker the shade, the lower (better) the p-value.

The default view only shows predicted binding sites with scores of 400 or greater but can be adjusted in the track settings. Multi-select filters allow viewing of particular transcription factors. At window sizes of greater than 10,000 base pairs, this track turns to density graph mode. Zoom to a smaller region and click into an item to see more detail.

From BED format documentation:

Conversion table:

Methods

JASPAR contains transcription factor binding sites with additional transcription factor profiles. TFBS predictions were selected with a PWM relative score ≥ 0.8 and a p-value < 0.05. P-values were scaled between 0 (corresponding to a p-value of 1) and 1000 (p-value ≤ 10^-10) for coloring of the genome tracks and to allow for comparison of prediction confidence between different profiles. More information on the methods can be found in their publications or on the JASPAR website.

Data Access

JASPAR Transcription Factor Binding data can be explored interactively with the Table Browser and cross-referenced with Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. JASPAR annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large.

All data are freely available. Additional resources are available directly from the JASPAR group:

• Binding site predictions for all and individual TF profiles are available for download at http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/.
• Code and data used to create the UCSC tracks are available at https://github.com/wassermanlab/JASPAR-UCSC-tracks.
• The underlying JASPAR motif data is available through the JASPAR website at https://jaspar.genereg.net/.

Other Genomes

The JASPAR group provides TFBS predictions for many additional species and genomes, accessible by connection to their Public Hub or by clicking the assembly links below:

Credits

The JASPAR database is a joint effort between several labs (please see the latest JASPAR paper, below). Binding site predictions and UCSC tracks were computed by the Wasserman Lab. For enquiries about the data please contact Oriol Fornes ( oriol@cmmt. ubc.ca ).

Wasserman Lab
Centre for Molecular Medicine and Therapeutics
BC Children's Hospital Research Institute
Department of Medical Genetics
University of British Columbia
Vancouver, Canada

References

Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2021 Nov 30;. PMID: 34850907

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020 Jan 8;48(D1):D87-D92. PMID: 31701148; PMC: PMC7145627