For each TF binding profile in the JASPAR database CORE collection, genomes were scanned for matches.
For the computation of relative scores and p-values, we used PWMScan (Ambrosini et al. 2018). We selected 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.
-JASPAR 2026 features a deep learning (DL) collection, providing a paradigm shift in modeling -and characterizing TF-DNA interactions with 1259 BPNet models trained on Homo sapiens ENCODE -chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from 240 TFs and -interpreted to reveal predictive motif patterns for the models. The motifs associated with -the same TF were clustered to provide a summary of the binding properties, resulting in -240 primary and 113 alternative motif patterns in the DL collection. See the JASPAR 2026 publication -for more information.
+The JASPAR 2026 update expanded the JASPAR CORE collection by 12% (306 +added or upgraded profiles), culminating to a set of 2633 non-redundant +TF binding profiles. Genome sequences were scanned with JASPAR 2026 +CORE TF binding profiles for each taxon 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 coloring of the genome +tracks and to allow for comparison of prediction confidence between +different profiles. More information on the methods can be found in the +JASPAR 2026 +publication or on the +JASPAR website. +The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). The new profiles were introduced after manual curation, in which 26 629 TF binding motifs were curated and obtained as PFMs or discovered from ChIP-seq/-exo or DAP-seq data. 2500 profiles from JASPAR 2022 were revised to either promote them to the CORE collection, update the associated metadata, or remove them because of validation inconsistencies or poor quality. The JASPAR database stores and focuses mostly on PFMs as the model of choice for TF-DNA interactions. More information on the methods can be found in the JASPAR 2024 publication or on the JASPAR website.
JASPAR 2022 contains updated transcription factor binding sites with additional transcription factor profiles. More information on the methods can be found in the @@ -254,33 +259,51 @@ href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">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 CBGR team at NCMBM using code developed at the Wasserman Lab. For enquiries about the data, -please contact Anthony Mathelier ( -) or Ieva Rauluseviciute ( -). +please contact Anthony Mathelier ( + +anthony. +mathelier@ncmbm. +uio. +no + +) or Ieva Rauluseviciute ( + +ieva. +rauluseviciute@ncmbm. +uio. +no + +).
CBGR
Computational Biology & Gene Regulation
Norwegian Centre for Molecular Biosciences and Medicine (NCMBM)
University of Oslo
Oslo, Norway
Wasserman Lab
Centre for Molecular Medicine and Therapeutics
BC Children's Hospital Research Institute
Department of Medical Genetics