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Adrien Bessy – One of the best experts on this subject based on the ideXlab platform.

  • JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Robin Van der lee, Francois Parcy, Oriol Fornes, Aziz Khan, Arnaud Stigliani, Marius Gheorghe, Robin Van Der Lee, Benoit Ballester, Jaime Castro-mondragon, Adrien Bessy

    Abstract:

    Erratum JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework.

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  • jaspar 2018 update of the open Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castromondragon, Robin Van Der Lee, Adrien Bessy, Jeanne Cheneby, Shubhada Rajabhau Kulkarni

    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) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

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Oriol Fornes – One of the best experts on this subject based on the ideXlab platform.

  • jaspar 2018 update of the open Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castromondragon, Robin Van Der Lee, Adrien Bessy, Jeanne Cheneby, Shubhada Rajabhau Kulkarni

    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) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

    Free Register to Access Article

  • JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Robin Van der lee, Francois Parcy, Oriol Fornes, Aziz Khan, Arnaud Stigliani, Marius Gheorghe, Robin Van Der Lee, Benoit Ballester, Jaime Castro-mondragon, Adrien Bessy

    Abstract:

    Erratum JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework.

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  • jaspar 2016 a major expansion and update of the open Access Database of transcription factor binding profiles
    Nucleic Acids Research, 2016
    Co-Authors: Anthony Mathelier, David J Arenillas, Chihyu Chen, Oriol Fornes, Grégoire Denay, Jessica J Y Lee, Wenqiang Shi, Casper Shyr, Ge Tan, Rebecca Worsleyhunt

    Abstract:

    JASPAR (http://jaspar.genereg.net) is an open-Access Database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic Access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.

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Aziz Khan – One of the best experts on this subject based on the ideXlab platform.

  • JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Robin Van der lee, Francois Parcy, Oriol Fornes, Aziz Khan, Arnaud Stigliani, Marius Gheorghe, Robin Van Der Lee, Benoit Ballester, Jaime Castro-mondragon, Adrien Bessy

    Abstract:

    Erratum JASPAR 2018: update of the open-Access Database of transcription factor binding profiles and its web framework.

    Free Register to Access Article

  • jaspar 2018 update of the open Access Database of transcription factor binding profiles and its web framework
    Nucleic Acids Research, 2018
    Co-Authors: Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castromondragon, Robin Van Der Lee, Adrien Bessy, Jeanne Cheneby, Shubhada Rajabhau Kulkarni

    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) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

    Free Register to Access Article