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

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-Garcia; Ge Tan; Jeanne Chèneby; Benoit Ballester; François Parcy; Albin Sandelin; Boris Lenhard; Wyeth W Wasserman; Anthony Mathelier

doi:10.1093/nar/gkz1001

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

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-Garcia, Ge Tan, Jeanne Chèneby, Benoit Ballester, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W Wasserman, Anthony Mathelier

Bioinformatik og RNA Biologi

247 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gkz1001
Status	Udgivet - 1 jan. 2020

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10.1093/nar/gkz1001

gkz1001.pdfForlagets udgivne version, 978 KBLicens: CC BY-NC

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Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., Santana-Garcia, W., Tan, G., Chèneby, J., Ballester, B., Parcy, F., Sandelin, A., Lenhard, B., Wasserman, W. W., & Mathelier, A. (2020). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz1001

Fornes, O, Castro-Mondragon, JA, Khan, A, van der Lee, R, Zhang, X, Richmond, PA, Modi, BP, Correard, S, Gheorghe, M, Baranašić, D, Santana-Garcia, W, Tan, G, Chèneby, J, Ballester, B, Parcy, F, Sandelin, A, Lenhard, B, Wasserman, WW & Mathelier, A 2020, 'JASPAR 2020: update of the open-access database of transcription factor binding profiles', Nucleic Acids Research. https://doi.org/10.1093/nar/gkz1001

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title = "JASPAR 2020: update of the open-access database of transcription factor binding profiles",

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.",

author = "Oriol Fornes and Castro-Mondragon, {Jaime A} and Aziz Khan and {van der Lee}, Robin and Xi Zhang and Richmond, {Phillip A} and Modi, {Bhavi P} and Solenne Correard and Marius Gheorghe and Damir Barana{\v s}i{\'c} and Walter Santana-Garcia and Ge Tan and Jeanne Ch{\`e}neby and Benoit Ballester and Fran{\c c}ois Parcy and Albin Sandelin and Boris Lenhard and Wasserman, {Wyeth W} and Anthony Mathelier",

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year = "2020",

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doi = "10.1093/nar/gkz1001",

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AU - Fornes, Oriol

AU - Castro-Mondragon, Jaime A

AU - Khan, Aziz

AU - van der Lee, Robin

AU - Zhang, Xi

AU - Richmond, Phillip A

AU - Modi, Bhavi P

AU - Correard, Solenne

AU - Gheorghe, Marius

AU - Baranašić, Damir

AU - Santana-Garcia, Walter

AU - Tan, Ge

AU - Chèneby, Jeanne

AU - Ballester, Benoit

AU - Parcy, François

AU - Sandelin, Albin

AU - Lenhard, Boris

AU - Wasserman, Wyeth W

AU - Mathelier, Anthony

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N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkz1001

DO - 10.1093/nar/gkz1001

M3 - Journal article

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JO - Nucleic Acids Research

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ER -

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

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