JASPAR Genome Browser tracks

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Genome Browser track data hub containing genome-wide binding site predictions for TF profiles in the JASPAR CORE.

Introduction

We scanned the genomes of 8 organisms (A. thaliana, C. elegans, C. intestinalis, D. rerio, D. melanogaster, H. sapiens, M. musculus, and S. cerevisiae) with the JASPAR CORE PFMs associated with the same taxon to predict TFBSs and create the JASPAR TFBS genomic tracks. Moreover, we created a collection of familial TFBSs by merging overlapping TFBSs that were predicted from PFMs associated with the same familial binding profile. The TFBS predictions associated with all PFMs are available here.

We provide JASPAR TFBS predictions as genomic tracks, which can be visualized in genome browsers. Notably, the UCSC Genome Browser now presents predicted human JASPAR TFBS data as a native track for the human genome with information such as TF names, TFBS prediction scores, and PFM logo for each of the 12+ billion predictions.

The code and data used to create the UCSC tracks can be found at https://github.com/wassermanlab/JASPAR-UCSC-tracks.

Table of contents

UCSC tracks

Native tracks

Since the 2022 JASPAR release, the TFBSs are accessible as native UCSC genome tracks.

Familial binding sites tracks

Genomic tracks can be viewed directly in the UCSC genome browser by connecting to the Public Hubs (Figure 1). The following genome assemblies are available and accessible directly by clicking on the assembly:

  • Arabidopsis thaliana: araTha1
  • Caenorhabditis elegans: ce10
  • Caenorhabditis elegans: ce11
  • Ciona intestinalis: ci3
  • Danio rerio: danRer11
  • Drosophila melanogaster: dm6
  • Homo sapiens: hg19
  • Homo sapiens: hg38
  • Mus musculus: mm10
  • Mus musculus: mm39
  • Saccharomyces cerevisiae: sacCer3

Download

Underlying TFBS prediction data is available for download and further analysis: http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/

Example of dataset (random sample of lines):

chr1    280     298     AGL3    821     369     -
chr1    309     327     AGL3    823     373     +
chr1    309     327     AGL3    882     488     -
chr1    1577    1595    AGL3    823     373     +
chr1    1577    1595    AGL3    883     490     -
chr1    2113    2131    AGL3    853     428     +
chr1    3186    3204    AGL3    825     376     -
chr1    3543    3561    AGL3    834     392     +
chr1    4284    4302    AGL3    824     375     +
chr1    4302    4320    AGL3    838     399     -
chr1    4318    4336    AGL3    818     365     -
chr1    4386    4404    AGL3    826     378     -
chr1    4908    4926    AGL3    838     399     -
chr1    6799    6817    AGL3    811     354     -
chr1    7097    7115    AGL3    810     352     +
chr1    7339    7357    AGL3    829     383     -
chr1    8054    8072    AGL3    802     339     +
chr1    8054    8072    AGL3    815     359     -
chr1    8097    8115    AGL3    898     525     +
chr1    8097    8115    AGL3    945     665     -

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Ensembl tracks

Direct link

View the tracks directly in the Ensembl Genome Browser using this link.

Attach track hub

You can attach the JASPAR track hub to Ensembl via “Configure this page”. Then search the Track Hub Repository for JASPAR and attach the hub.

Note that while the JASPAR UCSC tracks by default show predicted TF binding sites with scores of 500 or greater (P < 10-5), the Ensembl tracks show all predicted binding sites. Ensembl colors predictions according to their score, from yellow (low scores) to green (medium) and blue (high). Please refer to the JASPAR hub help page (see below).

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Track Hub Registry

JASPAR genome tracks are also available in Track Hub Registry. Use this link and select the track for the assembly of interest.

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Further information

Click on the JASPAR track details within the UCSC Genome browser to view the track help page:

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