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JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework

(2018) NUCLEIC ACIDS RESEARCH. 46(D1). p.D260-D266
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
SITE PREDICTIONS, GENOME, ARABIDOPSIS, BIOINFORMATICS, REPRESENTATION, SPECIFICITIES, EXPRESSION, LANDSCAPE, DIVERSITY, DISCOVERY

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Citation

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Chicago
Khan, Aziz, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, et al. 2018. “JASPAR 2018 : Update of the Open-access Database of Transcription Factor Binding Profiles and Its Web Framework.” Nucleic Acids Research 46 (D1): D260–D266.
APA
Khan, Aziz, Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., et al. (2018). JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework. NUCLEIC ACIDS RESEARCH, 46(D1), D260–D266.
Vancouver
1.
Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, et al. JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework. NUCLEIC ACIDS RESEARCH. 2018;46(D1):D260–D266.
MLA
Khan, Aziz, Oriol Fornes, Arnaud Stigliani, et al. “JASPAR 2018 : Update of the Open-access Database of Transcription Factor Binding Profiles and Its Web Framework.” NUCLEIC ACIDS RESEARCH 46.D1 (2018): D260–D266. Print.
@article{8558108,
  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.},
  author       = {Khan, Aziz and Fornes, Oriol and Stigliani, Arnaud and Gheorghe, Marius and Castro-Mondragon, Jaime A and van der Lee, Robin and Bessy, Adrien and Cheneby, Jeanne and Kulkarni, Shubhada Rajabhau and Tan, Ge and Baranasic, Damir and Arenillas, David J and Sandelin, Albin and Vandepoele, Klaas and Lenhard, Boris and Ballester, Benoit and Wasserman, Wyeth W and Parcy, Francois and Mathelier, Anthony},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {SITE PREDICTIONS,GENOME,ARABIDOPSIS,BIOINFORMATICS,REPRESENTATION,SPECIFICITIES,EXPRESSION,LANDSCAPE,DIVERSITY,DISCOVERY},
  language     = {eng},
  number       = {D1},
  pages        = {D260--D266},
  title        = {JASPAR 2018 : update of the open-access database of transcription factor binding profiles and its web framework},
  url          = {http://dx.doi.org/10.1093/nar/gkx1126},
  volume       = {46},
  year         = {2018},
}

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