JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Anthony Mathelier; Xiaobei Zhao; Allen W. Zhang; François Parcy; Rebecca Worsley-Hunt; David J. Arenillas; Sorana Buchman; Chih-yu Chen; Alice Chou; Hans-Ioan Ienasescu; Jonathan Lim; Casper Shyr; Ge Tan; Michelle Zhou; Boris Lenhard; Albin Gustav Sandelin; Wyeth W Wasserman

doi:10.1093/nar/gkt997

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Anthony Mathelier, Xiaobei Zhao, Allen W. Zhang, François Parcy, Rebecca Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih-yu Chen, Alice Chou, Hans-Ioan Ienasescu, Jonathan Lim, Casper Shyr, Ge Tan, Michelle Zhou, Boris Lenhard, Albin Gustav Sandelin, Wyeth W Wasserman

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Abstract

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

Original language	English
Journal	Nucleic Acids Research
Volume	42
Pages (from-to)	D142-D147
Number of pages	6
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkt997
Publication status	Published - 1 Jan 2014

Keywords

Animals
Arabidopsis
Binding Sites
Caenorhabditis elegans
Databases, Genetic
Drosophila melanogaster
Humans
Internet
Mice
Position-Specific Scoring Matrices
Regulatory Elements, Transcriptional
Transcription Factors

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JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profilesFinal published version, 3.15 MB

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Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C., Chou, A., Ienasescu, H.-I., Lim, J., Shyr, C., Tan, G., Zhou, M., Lenhard, B., Sandelin, A. G., & Wasserman, W. W. (2014). JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research, 42, D142-D147. https://doi.org/10.1093/nar/gkt997

Mathelier, A, Zhao, X, Zhang, AW, Parcy, F, Worsley-Hunt, R, Arenillas, DJ, Buchman, S, Chen, C, Chou, A, Ienasescu, H-I, Lim, J, Shyr, C, Tan, G, Zhou, M, Lenhard, B, Sandelin, AG & Wasserman, WW 2014, 'JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles', Nucleic Acids Research, vol. 42, pp. D142-D147. https://doi.org/10.1093/nar/gkt997

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AB - JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

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KW - Arabidopsis

KW - Binding Sites

KW - Caenorhabditis elegans

KW - Databases, Genetic

KW - Drosophila melanogaster

KW - Humans

KW - Internet

KW - Mice

KW - Position-Specific Scoring Matrices

KW - Regulatory Elements, Transcriptional

KW - Transcription Factors

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SP - D142-D147

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JF - Nucleic Acids Research

ER -

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Abstract

Keywords

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