2017
DOI: 10.1093/nar/gkx1126
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

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 … Show more

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Cited by 1,292 publications
(917 citation statements)
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References 41 publications
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“…In silico analysis to search for potential Sp1 and Sp3 binding sites at the Per1 and Per2 promoters was done using the JASPAR database (46).…”
Section: Methylation Specific Pcr (Ms-pcr)mentioning
confidence: 99%
“…In silico analysis to search for potential Sp1 and Sp3 binding sites at the Per1 and Per2 promoters was done using the JASPAR database (46).…”
Section: Methylation Specific Pcr (Ms-pcr)mentioning
confidence: 99%
“…These results demonstrate the importance of YAMDA’s linear time seeding; a simple linear speedup of the MEME algorithm is not sufficient since its base runtime grows too fast. Moreover, all of the YAMDA and MEME example output motifs display significant similarity false(E<107false) to known motifs in the JASPAR database (Khan et al , 2017) according to TOMTOM (Gupta et al , 2007). Visually, however, the YAMDA motifs more closely resemble the MEME motifs than the JASPAR motifs, especially for IRF4.…”
Section: Examplesmentioning
confidence: 99%
“…For example, DBDs can be composed of zinc-coordinating, basic helix-loop-helix, basic-leucine zipper, or helix-turn-helix DNA-binding structures. These DBDs selectively bind specific DNA sequences that range from 4-12 bp, and the DNA binding sequences favored by hundreds of TFs have been described (Hume et al, 2015; Jolma et al, 2013; Khan et al, 2018). Multiple TF molecules typically bind together at any one enhancer or promoter-proximal element.…”
Section: Introductionmentioning
confidence: 99%