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. 2024 Jan 5;52(D1):D174-D182.
doi: 10.1093/nar/gkad1059.

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

Ieva Rauluseviciute  1 , Rafael Riudavets-Puig  1 , Romain Blanc-Mathieu  2 , Jaime A Castro-Mondragon  1 , Katalin Ferenc  1 , Vipin Kumar  1 , Roza Berhanu Lemma  1 , Jérémy Lucas  2 , Jeanne Chèneby  3 , Damir Baranasic  4   5   6 , Aziz Khan  1   7 , Oriol Fornes  8 , Sveinung Gundersen  3 , Morten Johansen  3 , Eivind Hovig  3   9 , Boris Lenhard  4   5 , Albin Sandelin  10 , Wyeth W Wasserman  8 , François Parcy  2 , Anthony Mathelier  1   3   11
Affiliations

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

Ieva Rauluseviciute et al. Nucleic Acids Res. .

Abstract

JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs' structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Overview of the growth of the number of profiles in JASPAR CORE collection across releases and taxons.
Figure 2.
Figure 2.
TF binding profile trimming. (A, B) Examples of trimmed PFMs for FOXA1 (A) and Atoh7 (B) TFs with the logos of the original PFMs at the top and the logos of the trimmed PFMs at the bottom. (C) The number of trimmed positions varied from 1 to 19 for PFMs originating from JASPAR 2022. (D) The distribution of Gini coefficients computed on the IC of each position in the original (green) and trimmed (purple) PFMs from JASPAR 2022 exhibits a concentration of informative positions in the updated PFMs.
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