Description
This UCSC Genome Browser track hub represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the JASPAR database CORE collection.
Genomes
A list of genomes for which we provide predictions is available here.
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 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 |
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| 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 |
Methods
For each TF binding profile in the JASPAR CORE collection, genomes were scanned for matches.
For computation of relative scores and p-values, we use PWMScan (Ambrosini et al. 2018). We select TFBS predictions 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 colouring of the genome tracks and to allow for comparison of prediction confidence between different profiles.
Please refer to the supplementary information of the JASPAR 2020 manuscript for more details (citation below).
Data Availability
All data is freely available.
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 Wyeth Wasserman (wyeth@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
JASPAR 2020: update of the open-access database of transcription factor binding profiles. Submitted to Nucleic Acids Research.
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