JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

By Elodie Portales-Casamar, S. Thongjuea, Andrew Tae-Jun Kwon, David J. Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin. Nucleic Acids Res., 2009

641 citations recorded by the source corpus.

JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches.

Subfields: Molecular Biology

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Citations in the corpus

DNA-binding specificities of human transcription factors. (2013, neutral): “We next determined the fraction of high-confidence human TFs that are covered by models in our data and in existing databases, including a literature-curated set (JASPAR; Portales-Casamar et al., 2010), and a collection based on a high-throughput approach (PBMs; Badis et al.”
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, methodology): “Brieﬂy, a set of PWMs was collected from TRANSFAC (25), JASPAR (26), and protein-binding microarray (PBM) experiments (27–29).”
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (2017, methodology): “The PFMs were manually curated using independent external literature supporting the candidate TF-binding preferences, as previously described in (23).”
Cistrome: an integrative platform for transcriptional regulation studies (2011, methodology): “SeqPos can scan all of the motifs that we collected from JASPAR [25], TRANSFAC [26], Protein Binding Microarray (PBM) [27], Yeast-1-hybrid (y1h) [28], and the human proteinDNA interaction (hPDI) databases [29].”
Ensembl 2013 (2012, methodology): “Forty of these TFs have binding matrices available through the JASPAR database (33), and we have incorporated these motif data as positions of high probability TF-binding sites (5% False Nucleic Acids Research, 2013, Vol.”
RBPDB: a database of RNA-binding specificities (2010, methodology): “Collections of DNA-binding speciﬁcities of transcription factors are available and widely used (12,13); however, to our knowledge, there is no central repository of information on the RNA-binding activities of RBPs.”
AlleleSeq: analysis of allele-specific expression and binding in a network framework (2011, methodology): “The motif consensus sequences were generated from the PWMs (source TRANSFAC, Matys et al , 2006 and JASPAR, Portales-Casamar et al , 2010).”
AnimalTFDB: a comprehensive animal transcription factor database (2011, methodology): “TFs binding sites and target genes were extracted from TRED (19) and JASPAR (20) databases.”
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, methodology): “Known transcription factor binding matrices were downloaded from the JASPAR (18), Transfac (19), Cistrome (20) and UniPROBE (21) databases.”
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles (2015, methodology): “As in previous releases, we manually curated profiles with independent publications for TFBSs or profiles consistent with the candidates, as described in (12).”
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles (2013, methodology): “To confirm the putative binding patterns, we identified independent publications with TFBSs or profiles consistent with the candidates, as described in (7).”
Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population (2012, methodology): “To search for an enrichment of DNA binding motifs in the set of 435 a-DMR genes, we used PSCAN [29] with the JASPAR database [30].”
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014, methodology): “The collection of JASPAR vertebrate WMs plus, for each WM, the amino acid sequence of the TF that JASPAR associates with the WM [7].”
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013, methodology): “PWMs from TRANSFAC and JASPAR were used to scan the promoters of all human genes in the region − 2000 and +500 from the transcription factor start site (TSS).”
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles (2021, methodology): “In the 9th release of JASPAR, we discarded unused collections introduced in early releases of the database (27–29) that either did not correspond to TF-specific binding profiles or were data-type specific; we maintained the CORE and Unvalidated collections.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…2009 NetPath http://netpath.org Kandasamy et al., 2010 JASPAR Transcription factor–transcription factor binding information http://jaspar.genereg.net Portales-Casamar et al., 2010 HTRIdb http://www.lbbc.ibb.unesp.br/htri Bovolenta et al., 2012 MPromDB http://mpromdb.wistar.upenn.edu Gupta et al.,…”
Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, methodology): “The promoter analysis tools in Chipster offer a possibility to search for common sequence motifs with Wee-der [27] or Cosmo [28], or search for known transcription factor binding motifs using the JASPAR matrices [29].”