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

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Title: JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.
Authors: Khan, A
Fornes, O
Stigliani, A
Gheorghe, M
Castro-Mondragon, JA
Van der Lee, R
Bessy, A
Chèneby, J
Kulkarni, SR
Tan, G
Baranasic, D
Arenillas, DJ
Sandelin, A
Vandepoele, K
Lenhard, B
Ballester, B
Wasserman, WW
Parcy, F
Mathelier, A
Item Type: Journal Article
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.
Issue Date: 13-Nov-2017
Date of Acceptance: 27-Oct-2017
URI: http://hdl.handle.net/10044/1/53819
DOI: https://dx.doi.org/10.1093/nar/gkx1126
ISSN: 0305-1048
Publisher: Oxford University Press
Start Page: D260
End Page: D266
Journal / Book Title: Nucleic Acids Research
Volume: 46
Issue: D1
Copyright Statement: © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Sponsor/Funder: Biotechnology and Biological Sciences Research Council (BBSRC)
Wellcome Trust
Funder's Grant Number: BB/L00741X/1
106954/Z/15/Z
Keywords: 05 Environmental Sciences
06 Biological Sciences
08 Information And Computing Sciences
Developmental Biology
Publication Status: Published
Appears in Collections:Institute of Clinical Sciences