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

Abstract

JASP AR ( https://jaspar .elixir .no/) isã widely-used open-access database presenting manually curated high-qualityãnd non-redundant DNA-binding profiles for transcription factors (TFs)ãcross taxa. In this 10th releaseãnd 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profilesãnd provided orthogonal support for 72 profiles from the previous release's UNV ALID ATED collection. Altogether , the JASP AR 2024 update providesã 20% increase in CORE profiles from the previous release. A trimmingãlgorithm enhanced profiles by removing low information content flanking base pairs, which w ere lik ely uninf ormativ e (within the capacity of the PFM models) for TFBS predictionsãnd modelling TF-DNA interactions. This release includes enhanced metãdatã, featuringã refined classification for plant TFs' str uct ural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with humanãnd mouse tracksã vãilableãs native tracks in the UCSC Genome browser. All dataãreãvailable through the JASPAR web interfaceãnd programmatically through its APIãnd the updated Bioconductorãnd pyJASP AR packages. Finally ,ã new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.