JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

By Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime Abraham Castro-Mondragón, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R. Kulkarni, Ge Tan and 9 more. Nucleic Acids Res., 2017

987 citations recorded by the source corpus.

Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

Subfields: Cancer Research, Molecular Biology

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Citations in the corpus

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species (2019, methodology): “Users can select the species, cell type, chromosome and a particular enhancer, and the database will generate a summary table, which includes coordinate of the enhancer, GWAS SNPs (50) within the enhancer, TF binding motifs from JASPAR (51), associated super-enhancer, related disease and enhancer se”
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles (2023, methodology): “JASPAR’s ease of use was further facilitated by introducing the new web-interface and including the ‘JASPAR dynamic tour’ in 2018, which guides users through the typical tasks and novel features of the JASPAR website ( 20 ).”
Benchmark and integration of resources for the estimation of human transcription factor activities (2018, background): “2018) and JASPAR (version 2018) (Khan et al. 2018) repositories.”
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors (2018, methodology): “Furthermore, TFBS for 18,952 TFs of 51 species were integrated from HOCOMOCO (21), TRANSFAC, JASPAR (22) and CIS-BP databases.”
Transcription factors activate genes through the phase separation capacity of their activation domains (2018, background): “These DBDs selectively bind specific DNA sequences that range from 4 to 12 bp, and the DNA binding sequences favored by hundreds of TFs have been described (Hume et al., 2015; Jolma et al., 2013; Khan et al., 2018).”
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data (2019, methodology): “We collected an extensive set of 4104 positional weight matrices (PWMs) from various online sources [JASPAR (29), HOCOMOCO (30), SwissRegulon (31), UniPROBE (32) and CIS-BP (33)], representing experimentally derived transcription factor binding site motifs of 560 transcription factors (the…”