JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

TLDR

JASPAR is an open‑access database of manually curated, non‑redundant transcription factor binding profiles spanning six taxonomic groups. The release clusters profiles into familial groups, updates genome tracks for eight organisms (including UCSC native tracks for human and mouse), and makes data available via the JASPAR website, RESTful API, R/Bioconductor package, and a new Python package pyJASPAR. The 9th release expands the CORE collection by 341 new profiles (a 19 % increase), adds 298 Unvalidated profiles, revises DNA‑binding domain classification for plant TFs, introduces word clouds for TF knowledge, and offers a new enrichment analysis tool.

Abstract

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.