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 shows only 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

The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). The new profiles were introduced after manual curation, in which 26 629 TF binding motifs were curated and obtained as PFMs or discovered from ChIP-seq/-exo or DAP-seq data. 2500 profiles from JASPAR 2022 were revised to either promote them to the CORE collection, update the associated metadata, or remove them because of validation inconsistencies or poor quality. The JASPAR database stores and focuses mostly on PFMs as the model of choice for TF-DNA interactions. More information on the methods can be found in the JASPAR 2024 publication or on the JASPAR website.

JASPAR 2022 contains updated transcription factor binding sites with additional transcription factor profiles. More information on the methods can be found in the JASPAR 2022 publication JASPAR 2022 publication or on the JASPAR website.

JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles for each taxa independently using PWMScan. 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.

JASPAR 2018 used the TFBS Perl module (Lenhard and Wasserman 2002) and FIMO (Grant, Bailey, and Noble 2011), as distributed within the MEME suite (version 4.11.2) (Bailey et al. 2009). For scanning genomes with the BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a relative score ≥ 0.8. For the FIMO scan, profiles were reformatted to MEME motifs and matches with a p-value < 0.05 were kept. TFBS predictions that were not consistent between the two methods (TFBS Perl module and FIMO) were removed. The remaining TFBS predictions were colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.

Please refer to the JASPAR 2024, 2022, 2020, and 2018 publications for more details (citation below).

Data Access

JASPAR Transcription Factor Binding data includes billions of items. Limited regions can be explored interactively with the Table Browser and cross-referenced with Data Integrator, although positional queries that are too big can lead to timing out. This results in a black page or truncated output. In this case, you may try reducing the chromosomal query to a smaller window.

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.

The utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options.

• bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values.
• bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options.

Example: retrieve all JASPAR items in chr1:200001-200400

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mm39/jaspar/JASPAR2024.bb -chrom=chr1 -start=200000 -end=200400 stdout

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

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. PMID: 29140473; PMC: PMC5753243

Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D et al. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2023 Nov 14;. PMID: 37962376