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 compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

Histone deacetylase inhibitors induce the expression of tumor suppressor genes Per1 and Per2 in human gastric cancer cells

“…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).…”

YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU

“…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 $false(E<{10}^{-7}false)$ 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.…”

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

“…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.…”