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Jaime Abraham Castro-Mondragon, Rafael Riudavets Puig, Ieva Rauluševičiūtė, Roza Berhanu Lemma, Laura Turchi, Romain Blanc‐Mathieu, Jérémy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez and 13 more
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.
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Castro-Mondragon, J. A., Puig, R. R., Rauluševičiūtė, I., Lemma, R. B., Turchi, L., Blanc‐Mathieu, R., Lucas, J., Boddie, P., Khan, A., Pérez, N. M., Fornés, O., Leung, T. Y., Aguirre, A., Hammal, F., Schmelter, D., Baranas̆ić, D., Ballester, B., Sandelin, A., Lenhard, B., … Mathelier, A. (2021). 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
Castro-Mondragon, Jaime Abraham, et al. "JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles." Nucleic Acids Research, vol. 50, no. D1, 2021, pp. D165–D173, https://doi.org/10.1093/nar/gkab1113.
Castro-Mondragon, Jaime Abraham, Rafael Riudavets Puig, Ieva Rauluševičiūtė, Roza Berhanu Lemma, Laura Turchi, Romain Blanc‐Mathieu, Jérémy Lucas, et al. "JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles." Nucleic Acids Research 50, no. D1 (2021): D165–D173. https://doi.org/10.1093/nar/gkab1113.
Castro-Mondragon J. A., Puig R. R., Rauluševičiūtė I. [и др.] JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles // Nucleic Acids Research. — 2021. — Vol. 50, № D1. — P. D165–D173. — URL: https://doi.org/10.1093/nar/gkab1113
@article{castromondragon2021jaspar,
title = {{JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles}},
author = {Jaime Abraham Castro-Mondragon and Rafael Riudavets Puig and Ieva Rauluševičiūtė and Roza Berhanu Lemma and Laura Turchi and Romain Blanc‐Mathieu and Jérémy Lucas and Paul Boddie and Aziz Khan and Nicolás Manosalva Pérez and Oriol Fornés and Tiffany Y. Leung and Alejandro Aguirre and Fayrouz Hammal and Daniel Schmelter and Damir Baranas̆ić and Benoît Ballester and Albin Sandelin and Boris Lenhard and Klaas Vandepoele and Wyeth W. Wasserman and François Parcy and Anthony Mathelier},
journal = {Nucleic Acids Research},
year = {2021},
volume = {50},
number = {D1},
pages = {D165--D173},
doi = {10.1093/nar/gkab1113},
url = {https://doi.org/10.1093/nar/gkab1113}
}TY - JOUR AU - Castro-Mondragon, Jaime Abraham AU - Puig, Rafael Riudavets AU - Rauluševičiūtė, Ieva AU - Lemma, Roza Berhanu AU - Turchi, Laura AU - Blanc‐Mathieu, Romain AU - Lucas, Jérémy AU - Boddie, Paul AU - Khan, Aziz AU - Pérez, Nicolás Manosalva AU - Fornés, Oriol AU - Leung, Tiffany Y. AU - Aguirre, Alejandro AU - Hammal, Fayrouz AU - Schmelter, Daniel AU - Baranas̆ić, Damir AU - Ballester, Benoît AU - Sandelin, Albin AU - Lenhard, Boris AU - Vandepoele, Klaas AU - Wasserman, Wyeth W. AU - Parcy, François AU - Mathelier, Anthony TI - JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles JO - Nucleic Acids Research VL - 50 IS - D1 SP - D165 EP - D173 PY - 2021 DA - 2021/10/22 DO - 10.1093/nar/gkab1113 UR - https://doi.org/10.1093/nar/gkab1113 ER -
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