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

TLDR

JASPAR is a widely‑used open‑access database that provides manually curated, high‑quality, non‑redundant DNA‑binding profiles for transcription factors across taxa. This 10th release and 20th‑anniversary update expands the CORE collection with 329 new profiles. The update incorporated new and refined profiles, applied a trimming algorithm to remove low‑information flanking bases, expanded metadata for plant TFs, and made data available via the web interface, API, Bioconductor, pyJASPAR, and a new TFBS extraction tool. The update yields a 20% increase in CORE profiles and updates TFBS tracks in eight organisms, including native tracks for human and mouse in the UCSC Genome Browser.

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.