-For each TF binding profile in the JASPAR CORE collection, genomes were -scanned in parallel using the best software available at the time.
-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 +(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 (24). We selected TFBS predictions -with a PWM relative score ≥ 0.8 and a p-value < 0.05. P-values were scaled +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).
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 interacted with through command line utilities. Please be aware that these download files are very large, between 75Gb and 86Gb.
-All data is freely available. +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 @@ -205,29 +202,39 @@ 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
-Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, -Correard S, Gheorghe M, Baranasic D, Santana-Garcia W, Tan G, Cheneby J, Ballester B, - Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. -JASPAR 2020: update of the open-access database of transcription factor binding -profiles. Nucleic Acids Res. 2020 . -PMID 31701148
+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 +Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, -Bessy A, Cheneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, -Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. -JASPAR 2018: update of the open-access database of transcription factor -binding profiles and its web framework. Nucleic Acids Research. -2018. PMID 29140473
+Bessy A, Chèneby J, Kulkarni SR, Tan G et al. + +JASPAR 2018: update of the open-access database of transcription factor +binding profiles and its web framework. +Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. +PMID: 29140473; PMC: PMC5753243 +