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

Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, et al.
(2022) NUCLEIC ACIDS RESEARCH. 50(D1). p.D165-D173
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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.
Keywords
Genetics, DNA SHAPE-FEATURES, ENRICHMENT ANALYSIS, MOTIF DATABASE, TFBSSHAPE, MOUSE, TOOLS, GENE

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Citation

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MLA
Castro-Mondragon, Jaime A., et al. “JASPAR 2022 : The 9th Release of the Open-Access Database of Transcription Factor Binding Profiles.” NUCLEIC ACIDS RESEARCH, vol. 50, no. D1, 2022, pp. D165–73, doi:10.1093/nar/gkab1113.
APA
Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Berhanu Lemma, R., Turchi, L., Blanc-Mathieu, R., … Mathelier, A. (2022). JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles. NUCLEIC ACIDS RESEARCH, 50(D1), D165–D173. https://doi.org/10.1093/nar/gkab1113
Chicago author-date
Castro-Mondragon, Jaime A, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, et al. 2022. “JASPAR 2022 : The 9th Release of the Open-Access Database of Transcription Factor Binding Profiles.” NUCLEIC ACIDS RESEARCH 50 (D1): D165–73. https://doi.org/10.1093/nar/gkab1113.
Chicago author-date (all authors)
Castro-Mondragon, Jaime A, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, and Anthony Mathelier. 2022. “JASPAR 2022 : The 9th Release of the Open-Access Database of Transcription Factor Binding Profiles.” NUCLEIC ACIDS RESEARCH 50 (D1): D165–D173. doi:10.1093/nar/gkab1113.
Vancouver
1.
Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, et al. JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles. NUCLEIC ACIDS RESEARCH. 2022;50(D1):D165–73.
IEEE
[1]
J. A. Castro-Mondragon et al., “JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles,” NUCLEIC ACIDS RESEARCH, vol. 50, no. D1, pp. D165–D173, 2022.
@article{8731751,
  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.}},
  author       = {{Castro-Mondragon, Jaime A and Riudavets-Puig, Rafael and Rauluseviciute, Ieva and Berhanu Lemma, Roza and Turchi, Laura and Blanc-Mathieu, Romain and Lucas, Jeremy and Boddie, Paul and Khan, Aziz and Manosalva Pérez, Nicolás and Fornes, Oriol and Leung, Tiffany Y and Aguirre, Alejandro and Hammal, Fayrouz and Schmelter, Daniel and Baranasic, Damir and Ballester, Benoit and Sandelin, Albin and Lenhard, Boris and Vandepoele, Klaas and Wasserman, Wyeth W and Parcy, François and Mathelier, Anthony}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{Genetics,DNA SHAPE-FEATURES,ENRICHMENT ANALYSIS,MOTIF DATABASE,TFBSSHAPE,MOUSE,TOOLS,GENE}},
  language     = {{eng}},
  number       = {{D1}},
  pages        = {{D165--D173}},
  title        = {{JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles}},
  url          = {{http://doi.org/10.1093/nar/gkab1113}},
  volume       = {{50}},
  year         = {{2022}},
}
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