JASPAR 2020: update of the open-access database of transcription factor binding profiles

JASPAR 2020: update of the open-access database of transcription factor binding profiles

2020 | Oriol Fornes, Jaime A. Castro-Mondragon, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip A. Richmond, Bhavi P. Modi, Solenne Correard, Marius Gheorghe, Damir Baranašić, Walter Santana-García, Ge Tan, Jeanne Chèneby, Benoit Ballester, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W. Wasserman, and Anthony Mathelier
JASPAR 2020 is an updated version of the open-access database of transcription factor (TF) binding profiles. The database includes position frequency matrices (PFMs) for TFs across six taxonomic groups. In this release, the CORE collection was expanded with 245 new PFMs, representing an 18% increase compared to the previous release. Additionally, 156 PFMs were updated. The database also includes a new collection of unvalidated TF-binding profiles, which are stored for which curators could not find orthogonal supporting evidence. This collection has a dedicated web interface for community curation. The database also includes a Q&A forum to facilitate communication between users and curators. The genomic tracks, inference tool, and TF-binding profile similarity clusters were updated. All data is available through the JASPAR website, its associated RESTful API, and the JASPAR2020 R/Bioconductor package. The JASPAR database has been maintained for over 15 years and is one of the most popular databases of TF-binding profiles. The database includes manually curated, non-redundant TF-binding profiles for TFs from six taxa. The database also includes TFFMs, which are hidden Markov-based models capturing dinucleotide dependencies in TF-DNA interactions. The database has been updated to include genomic tracks for 8 genomes and an improved inference tool. The database also includes hierarchical clusters of TF-binding profiles for each taxon. The JASPAR database is a valuable resource for researchers studying gene regulation and transcription factor binding.JASPAR 2020 is an updated version of the open-access database of transcription factor (TF) binding profiles. The database includes position frequency matrices (PFMs) for TFs across six taxonomic groups. In this release, the CORE collection was expanded with 245 new PFMs, representing an 18% increase compared to the previous release. Additionally, 156 PFMs were updated. The database also includes a new collection of unvalidated TF-binding profiles, which are stored for which curators could not find orthogonal supporting evidence. This collection has a dedicated web interface for community curation. The database also includes a Q&A forum to facilitate communication between users and curators. The genomic tracks, inference tool, and TF-binding profile similarity clusters were updated. All data is available through the JASPAR website, its associated RESTful API, and the JASPAR2020 R/Bioconductor package. The JASPAR database has been maintained for over 15 years and is one of the most popular databases of TF-binding profiles. The database includes manually curated, non-redundant TF-binding profiles for TFs from six taxa. The database also includes TFFMs, which are hidden Markov-based models capturing dinucleotide dependencies in TF-DNA interactions. The database has been updated to include genomic tracks for 8 genomes and an improved inference tool. The database also includes hierarchical clusters of TF-binding profiles for each taxon. The JASPAR database is a valuable resource for researchers studying gene regulation and transcription factor binding.
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