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

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 - 2018/1/1

Y1 - 2018/1/1

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

SN - 0305-1048

VL - 46

SP - D260-D266

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

M1 - gkx1126

ER -