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

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.

Figure 1.

JASPAR CORE collection growth. The number of non-redundant profiles in each taxon (see legend) and overall through all JASPAR releases.

Figure 2.

JASPAR TF word clouds. Webpage providing information about the binding profile associated with PAX6. The word cloud of terms obtained for PAX6 is highlighted in red, which supports the role of this TF in eye development and its implication in causing the genetic disorder aniridia.

Figure 3.

TFBS differential enrichment analysis on DNase-seq data for A549 cells before and after 2 h of dexamethasone treatment. Enrichment significance for each JASPAR profile from the vertebrate CORE collection is shown in the y-axis as -log₁₀(P) in this beeswarm plot. Each point depicts the Fisher exact test P-value (P) corresponding to a TF. The Points are colored based on the TF DBD structural family annotation, with a distinct color for each of the top 10 enriched families (see legend). Light yellow represents TF families outside of the top 10 enriched and with -log₁₀(P) > 3 (Other) and brown represents TF families for which -log₁₀(P) ≤ 3 (non significant, N.S.).