This track represents genome-wide predicted binding sites for TF
(transcription factor) binding profiles in the
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:
|score in range
JASPAR 2022 contains updated transcription factor binding sites
with additional transcription factor profiles. More information on
the methods can be found in their upcoming publication or on the
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
Please refer to the JASPAR 2022, 2020, and 2018 publications for more
details (citation below).
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
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
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
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/hg38/jaspar/JASPAR2022.bb -chrom=chr1 -start=200000 -end=200400 stdout
All data are freely available.
Additional resources are available directly from the JASPAR group:
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:
||Genome assembly versions
|Human - Homo sapiens
|Mouse - Mus musculus
|Zebrafish - Danio rerio
|Fruitfly - Drosophila melanogaster
|Nematode - Caenorhabditis elegans
|Vase tunicate - Ciona intestinalis
|Thale cress - Arabidopsis thaliana
|Yeast - Saccharomyces cerevisiae
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
Centre for Molecular Medicine and Therapeutics
BC Children's Hospital Research Institute
Department of Medical Genetics
University of British Columbia
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
Nucleic Acids Res. 2021 Nov 30;.
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
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