This track represents genome-wide predicted binding sites for TF (transcription factor) binding profiles in the -JASPAR +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. @@ -79,33 +79,34 @@
-JASPAR 2022 contains updates transcription factor binding sites +JASPAR 2022 contains updated transcription factor binding sites with additional transcription factor profiles. More information on -the methods can be found in the upcoming publication.
+the methods can be found in their upcoming publication or on the +JASPAR website.JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles for each taxa independently using PWMScan. 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.
JASPAR 2018 used 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, profiles were converted to PWMs and matches were kept with a relative score ≥ 0.8. For the FIMO scan, profiles were reformatted to MEME motifs @@ -152,33 +153,32 @@ Public Hub or by clicking the assembly links below:
| Species | Genome assembly versions | |
| Human - Homo sapiens | hg19, hg38 | |
| Mouse - Mus musculus | --mm10 | +mm10, +mm39 |
| Zebrafish - Danio rerio | danRer11 | |
| Fruitfly - Drosophila melanogaster | dm6 | |
| Nematode - Caenorhabditis elegans | ce10 |