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

By Ieva Rauluseviciute, Rafael Riudavets-Puig, Romain Blanc-Mathieu, Jaime Abraham Castro-Mondragón, Katalin Ferenc, Vipin Kumar, R. B. Lemma, J. Lucas, Jeanne Chèneby, Damir Baranasic and 10 more. Nucleic Acids Research, 2023

875 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1038f4783e64585a6cac9ee5eed4705ac021a257