This UCSC Genome Browser track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the JASPAR database CORE collection.
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. This can be adjusted by adjusting the track settings.
From https://genome.ucsc.edu/FAQ/FAQformat.html#format1:
| shade | |||||||||
| score in range | ≤ 166 | 167-277 | 278-388 | 389-499 | 500-611 | 612-722 | 723-833 | 834-944 | ≥ 945 |
Conversion table:
Track score |
p-value |
0 |
1 |
100 |
0.1 |
131 |
0.049 |
200 |
10-2 |
300 |
10-3 |
400 |
10-4 |
500 |
10-5 |
600 |
10-6 |
700 |
10-7 |
800 |
10-8 |
900 |
10-9 |
1000 |
≤ 10-10 |
For each TF binding profile in the JASPAR CORE collection, genomes were scanned in parallel using 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, we converted profiles to PWMs and kept matches 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 converted to genome tracks and colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.
Please refer to the JASPAR 2018 manuscript for more details (citation below).
All data is freely available.
The JASPAR group provides TFBS predictions for many additional species and genomes in their Public Hub:
+The JASPAR group provides TFBS predictions for many additional species and genomes in their Public Hub:
| Species | Genome assembly versions |
| Human | hg19, hg38 |
| Danio rerio | danRer10 |
| Drosophila melanogaster | dm6 |
| Caenorhabditis elegans | ce10 |
| Arabidopsis thaliana | araTha1 |
| Saccharomyces cerevisiae | sacCer3 |
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 and are maintained by David Arenillas (dave@cmmt.ubc.ca). For enquiries about the data please contact Oriol Fornes (oriol@cmmt.ubc.ca) and Robin van der Lee (rvdlee@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
A Khan, O Fornes, A Stigliani, A Bessy, M Gheorghe, R van der Lee, J A Castro-Mondragon, J Cheneby, S R Kulkarni, G Tan, D Baranasic, D J Arenillas, A Sandelin, K Vandepoele, B Lenhard, B Ballester, W W Wasserman, F Parcy, A Mathelier. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research. 2018. PMID 29140473