1. Direct link
View the tracks directly in the UCSC Genome Browser for the following species and genome assemblies:
- Human: hg19 and hg38
- Mus musculus: mm10
- Drosophila melanogaster: dm6
- Caenorhabditis elegans: ce10
- Danio rerio: danRer11
- Arabidopsis thaliana: araTha1
- Saccharomyces cerevisiae: sacCer3
2. Public track hub
Connect to the JASPAR track data Public Hub on the UCSC Genome Browser via "MyData => Track Hubs" by first searching for JASPAR, and then adding the hub to your session using "Connect" .
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):
1. Direct link
View the tracks directly in the Ensembl Genome Browser: http://www.ensembl.org/Trackhub?url=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt
2. 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).
- Code and data used to create the UCSC tracks are available at https://github.com/wassermanlab/JASPAR-UCSC-tracks
- For more information on the use of UCSC track data hubs, see Using UCSC Genome Browser Track Hubs
- For more information on the use of track hubs in Ensembl, see http://www.ensembl.org/info/website/adding_trackhubs.html