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. / Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A.; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R.; Tan, Ge; Baranasic, Damir; Arenillas, David J.; Sandelin, Albin Gustav; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony.
In: Nucleic Acids Research, Vol. 46, No. D1, gkx1126, 2018, p. D260-D266.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - JASPAR 2018
T2 - update of the open-access database of transcription factor binding profiles and its web framework
AU - Khan, Aziz
AU - Fornes, Oriol
AU - Stigliani, Arnaud
AU - Gheorghe, Marius
AU - Castro-Mondragon, Jaime A.
AU - van der Lee, Robin
AU - Bessy, Adrien
AU - Chèneby, Jeanne
AU - Kulkarni, Shubhada R.
AU - Tan, Ge
AU - Baranasic, Damir
AU - Arenillas, David J.
AU - Sandelin, Albin Gustav
AU - Vandepoele, Klaas
AU - Lenhard, Boris
AU - Ballester, Benoît
AU - Wasserman, Wyeth W.
AU - Parcy, François
AU - Mathelier, Anthony
N1 - Erratum: JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (vol 46, pg 260, 2017) DOI: 10.1093/nar/gkx1188
PY - 2018
Y1 - 2018
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) 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.
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) 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.
KW - Journal Article
U2 - 10.1093/nar/gkx1126
DO - 10.1093/nar/gkx1126
M3 - Journal article
C2 - 29140473
VL - 46
SP - D260-D266
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
M1 - gkx1126
ER -
ID: 185718895