JASPAR: an open-access database for eukaryotic transcription factor binding profiles

By Albin Sandelin, Wynand Alkema, Pär G. Engström, Wyeth W. Wasserman, Boris Lenhard. Nucleic Acids Res., 2004

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In Molecular Biology

Citations in the corpus

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort (2013, background): “An annotation effort typically starts with one of the scientific papers suggested in databases such as TFCat and JASPAR to document a candidate DbTF, or by searching for adequate literature in one of the following resources: UniProt (http:// www.uniprot.org/), NCBI’s Entrez Gene (25), iHOP (26), Gen”
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. (2008, background): “…on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA 4Banting and Best Department of Medical Research 5Department of Molecular Genetics University of Toronto, Toronto, ON M5S 3E1, Canada 6Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical…”
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.”
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, methodology): “To this aim, we first assembled a library of 338 position weight matrices (PWMs) by combining the DNA binding motifs in the Jaspar database [67] and those in a recently reported set of PWMs for 104 mouse transcription factors [68].”
A computational pipeline for comparative ChIP-seq analyses (2011, background): “com/product/transcription-factor-binding-sites , for which a freely available and a commercial version exist, and/or JASPA”
Detection of functional DNA motifs via statistical over-representation. (2004, methodology): “Consistent with this evidence, the Hunchback motif is signi®cantly over-represented, and although Kru Èppel is absent from Jaspar, the Kru Èppel-like factor Gklf is recovered (Table 5).”
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints (2012, methodology): “We collected known binding preference motifs from the TRANSFAC [50], JASPAR [51], and Uniprobe [52] databases.”
MEME: discovering and analyzing DNA and protein sequence motifs (2006, methodology): “By clicking on the button labeled “Compare PSPM to known motifs in JASPAR database” following each motif, the DNA motif can be compared to each of the motifs in the JASPAR database [9] of known TFBS motifs.”