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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles. / Castro-Mondragon, Jaime A.; Riudavets-Puig, Rafael; Rauluseviciute, Ieva; Lemma, Roza Berhanu; Turchi, Laura; Blanc-Mathieu, Romain; Lucas, Jeremy; Boddie, Paul; Khan, Aziz; Perez, Nicolás Manosalva; Fornes, Oriol; Leung, Tiffany Y.; Aguirre, Alejandro; Hammal, Fayrouz; Schmelter, Daniel; Baranasic, Damir; Ballester, Benoit; Sandelin, Albin; Lenhard, Boris; Vandepoele, Klaas; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony.

In: Nucleic acids symposium series, Vol. 50, No. D1, 2022, p. D165-D173.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Castro-Mondragon, JA, Riudavets-Puig, R, Rauluseviciute, I, Lemma, RB, Turchi, L, Blanc-Mathieu, R, Lucas, J, Boddie, P, Khan, A, Perez, NM, Fornes, O, Leung, TY, Aguirre, A, Hammal, F, Schmelter, D, Baranasic, D, Ballester, B, Sandelin, A, Lenhard, B, Vandepoele, K, Wasserman, WW, Parcy, F & Mathelier, A 2022, 'JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles', Nucleic acids symposium series, vol. 50, no. D1, pp. D165-D173. https://doi.org/10.1093/nar/gkab1113

APA

Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Lemma, R. B., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Perez, N. M., Fornes, O., Leung, T. Y., Aguirre, A., Hammal, F., Schmelter, D., Baranasic, D., Ballester, B., Sandelin, A., Lenhard, B., ... Mathelier, A. (2022). JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic acids symposium series, 50(D1), D165-D173. https://doi.org/10.1093/nar/gkab1113

Vancouver

Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Lemma RB, Turchi L, Blanc-Mathieu R et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic acids symposium series. 2022;50(D1):D165-D173. https://doi.org/10.1093/nar/gkab1113

Author

Castro-Mondragon, Jaime A. ; Riudavets-Puig, Rafael ; Rauluseviciute, Ieva ; Lemma, Roza Berhanu ; Turchi, Laura ; Blanc-Mathieu, Romain ; Lucas, Jeremy ; Boddie, Paul ; Khan, Aziz ; Perez, Nicolás Manosalva ; Fornes, Oriol ; Leung, Tiffany Y. ; Aguirre, Alejandro ; Hammal, Fayrouz ; Schmelter, Daniel ; Baranasic, Damir ; Ballester, Benoit ; Sandelin, Albin ; Lenhard, Boris ; Vandepoele, Klaas ; Wasserman, Wyeth W. ; Parcy, François ; Mathelier, Anthony. / JASPAR 2022 : the 9th release of the open-access database of transcription factor binding profiles. In: Nucleic acids symposium series. 2022 ; Vol. 50, No. D1. pp. D165-D173.

Bibtex

@article{674f9995065c4c96a0ad3cb1d82b25bb,
title = "JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles",
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 = "DNA SHAPE-FEATURES, ENRICHMENT ANALYSIS, MOTIF DATABASE, TFBSSHAPE, MOUSE, TOOLS, GENE",
author = "Castro-Mondragon, {Jaime A.} and Rafael Riudavets-Puig and Ieva Rauluseviciute and Lemma, {Roza Berhanu} and Laura Turchi and Romain Blanc-Mathieu and Jeremy Lucas and Paul Boddie and Aziz Khan and Perez, {Nicol{\'a}s Manosalva} and Oriol Fornes and Leung, {Tiffany Y.} and Alejandro Aguirre and Fayrouz Hammal and Daniel Schmelter and Damir Baranasic and Benoit Ballester and Albin Sandelin and Boris Lenhard and Klaas Vandepoele and Wasserman, {Wyeth W.} and Fran{\c c}ois Parcy and Anthony Mathelier",
year = "2022",
doi = "10.1093/nar/gkab1113",
language = "English",
volume = "50",
pages = "D165--D173",
journal = "Nucleic acids symposium series",
issn = "0261-3166",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - JASPAR 2022

T2 - the 9th release of the open-access database of transcription factor binding profiles

AU - Castro-Mondragon, Jaime A.

AU - Riudavets-Puig, Rafael

AU - Rauluseviciute, Ieva

AU - Lemma, Roza Berhanu

AU - Turchi, Laura

AU - Blanc-Mathieu, Romain

AU - Lucas, Jeremy

AU - Boddie, Paul

AU - Khan, Aziz

AU - Perez, Nicolás Manosalva

AU - Fornes, Oriol

AU - Leung, Tiffany Y.

AU - Aguirre, Alejandro

AU - Hammal, Fayrouz

AU - Schmelter, Daniel

AU - Baranasic, Damir

AU - Ballester, Benoit

AU - Sandelin, Albin

AU - Lenhard, Boris

AU - Vandepoele, Klaas

AU - Wasserman, Wyeth W.

AU - Parcy, François

AU - Mathelier, Anthony

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - DNA SHAPE-FEATURES

KW - ENRICHMENT ANALYSIS

KW - MOTIF DATABASE

KW - TFBSSHAPE

KW - MOUSE

KW - TOOLS

KW - GENE

U2 - 10.1093/nar/gkab1113

DO - 10.1093/nar/gkab1113

M3 - Journal article

C2 - 34850907

VL - 50

SP - D165-D173

JO - Nucleic acids symposium series

JF - Nucleic acids symposium series

SN - 0261-3166

IS - D1

ER -

ID: 297056593