+This track represents genome-wide predicted binding sites for TF +(transcription factor) binding profiles in the +JASPAR +CORE collection. This open-source database contains a curated, non-redundant +set of binding profiles derived from published collections of experimentally +defined transcription factor binding sites for eukaryotes.
+ ++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 in the track settings. Multi-select filters allow viewing of +particular transcription factors. At window sizes of greater than +10,000 base pairs, this track turns to density graph mode. +Zoom to a smaller region and click into an item to see more detail.
+ ++From BED format documentation: + +
| shade | ++ | + | + | + | + | + | + | + | + |
| score in range | +≤ 166 | +167-277 | +278-388 | +389-499 | +500-611 | +612-722 | +723-833 | +834-944 | +≥ 945 | +
Conversion table:
+| Item score | +0 | +100 | +131 | +200 | +300 | +400 | +500 | +600 | +700 | +800 | +900 | +1000 | +
| p-value | +1 | +0.1 | +0.049 | +10-2 | +10-3 | +10-4 | +10-5 | +10-6 | +10-7 | +10-8 | +10-9 | +≤ 10-10 | +
+JASPAR contains transcription factor binding sites +with additional transcription factor profiles. TFBS predictions were selected 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. More information on +the methods can be found in their publications or on the +JASPAR website.
+ ++JASPAR Transcription Factor Binding data can be explored interactively with the +Table Browser and cross-referenced with +Data Integrator. For programmatic access, +the track can be accessed using the Genome Browser's +REST API. +JASPAR annotations can be downloaded from the +Genome Browser's download server +as a bigBed file. This compressed binary format can be remotely queried through +command line utilities. Please note that some of the download files can be quite large.
+ ++All data are freely available. +Additional resources are available directly from the JASPAR group:
+The JASPAR group provides TFBS predictions for many additional species and +genomes, accessible by connection to their + +Public Hub or by clicking the assembly links below:
+| Species | +Genome assembly versions | +
| Human - Homo sapiens | +hg19, +hg38 | +
| Mouse - Mus musculus | ++ +mm10, +mm39 | +
| Zebrafish - Danio rerio | +danRer11 | +
| Fruitfly - Drosophila melanogaster | +dm6 | +
| Nematode - Caenorhabditis elegans | +ce10 | +
| Thale cress - Arabidopsis thaliana | +araTha1 | +
| Yeast - 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. For +enquiries about the data please contact Oriol Fornes +( +oriol@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 +
+Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, +Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, +Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, +Vandepoele K, Wasserman WW, Parcy F, and Mathelier A. JASPAR 2022: the 9th +release of the open-access database of transcription factor binding profiles +Nucleic Acids Res. Pending Publication. +
+ ++Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, +Modi BP, Correard S, Gheorghe M, Baranašić D et al. + +JASPAR 2020: update of the open-access database of transcription factor +binding profiles. +Nucleic Acids Res. 2020 Jan 8;48(D1):D87-D92. +PMID: 31701148; PMC: PMC7145627 +