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

By Anthony Mathelier, Xiaobei Zhao, Allen W. Zhang, François Parcy, R. Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih-Yu Chen, A. Chou, Hans Ienasescu and 7 more. Nucleic Acids Res., 2013

1,081 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2ad6572c5668fdb3b2375e32874dc0e7a64022f7

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Citations in the corpus

Ensembl 2015 (2014, methodology): “These features are annotated with transcription factor binding motifs from the 2014 release of the JASPAR database (16).”
Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing. (2017, methodology): “REAGENT or RESOURCE SOURCE IDENTIFIER Custom Perl script for off-target sites search This study NA SeqMan DNASTAR Lasergene http://www.dnastar.com CoGe Gevo tool (Lyons and Freeling, 2008) https://www.genomevolution.org/coge/ mVISTA (Mathelier et al., 2014) http://genome.lbl.gov/vista/mvista/about.s”
Ensembl regulation resources (2016, methodology): “We therefore annotate TF binding peaks with overlapping motif features, i.e. putative TFBS based on existing publicly TFBS Position Weight Matrices (PWM) from JASPAR (37).”
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (2019, methodology): “TarBase (19) and miRTarbase (20) have been used to obtain experimentally validated miRNA–gene target information, while ENCODE (21), JASPAR (22) and CHEA (23) have been used to obtain TF–gene target Users can double click a meta-node (large semi-transparent circles) to view all its associated genes ”
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis (2017, methodology): “Specifically, the compulsory curation of the discovered models is dependent on external data, e.g. UniProt (37), TF Encyclopedia (38), and the JAS-PAR database (39,40), which we consulted at the model curation stage.”
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions (2014, background): “TFBSshape describes the structural features of DNA at TF binding sites, and has entries for proteins corresponding to entries in JASPAR (34,35) and UniPROBE.”
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles (2023, methodology): “We further provide different interfaces ranging from straightforward web-interface to programmatic access through various packages in Perl ( 16 ), Python ( 17 ), R / Bioconductor ( 18 ), and Ruby ( 12 ).”
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2015, methodology): “Two other well-known TFBS repositories, PLACE and JASPAR, were created to facilitate the identification of TFBSs in input sequences (3,4).”