TFBS predictions in Arabidopsis thaliana (araTha1) for all profiles in the JASPAR CORE plants collection (2022) (MA1081.2)
 
Item: MA1081.2
Score: 400
Position: chr1:20727439-20727454
Genomic Size: 16
Strand: +
View DNA for this feature (araTha1/thale cress)

TF nameWRKY25
View table schema

Go to JASPAR2022 TFBS araTha1 track controls


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                  
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 2022: the 9th release of the open-access database of transcription factor binding profiles. Submitted to Nucleic Acids Research.