JASPAR 2020: update of the open-access database of transcription factor binding profiles
By Oriol Fornes, Jaime Abraham Castro-Mondragón, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A. Richmond, B. Modi, S. Correard, Marius Gheorghe, Damir Baranasic and 9 more. Nucleic Acids Res., 2019
1,745 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) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/22eff85986d301b074f4f1a243d3640f387f18b3
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In Cancer Research
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Citations in the corpus
- ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis (2021, methodology): “ArchR natively supports access to motif sets curated from chromVAR 16 and JASPAR 52 to be used for these motif analyses.”
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles (2023, methodology): “In 2020, we complemented the JASPAR CORE collection with the UNVAL-IDATED collection to reflect the increase in profiles derived from the broader use of high-throughput sequencing methods for which independent validation is yet to be produced ( 13 ).”
- miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology (2020, methodology): “The interactions among miRNAs, TFs and genes are obtained from TransmiR 2.0 (30), ENCODE (31), JASPAR (32) and ChEA (33).”