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 @@ -80,50 +79,57 @@
+JASPAR 2022 contains updates transcription factor binding sites +with additional transcription factor profiles. More information on +the methods can be found in the upcoming publication.
+ ++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 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 colored according to their FIMO p-value to allow for comparison of prediction confidence between different profiles.
--For JASPAR 2020, DNA sequences were scanned 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.
-Please refer to the JASPAR 2020 and 2018 publication for more details (citation below).
+Please refer to the JASPAR 2022, 2020, and 2018 publications for more +details (citation below).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. @@ -141,31 +147,32 @@
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: