TF binding site predictions - JASPAR CORE collection (2018)

These data are the basis of the JASPAR UCSC track hub, but can also be used independently. Detailed information at http://jaspar.genereg.net/genome-tracks/ and the track hub help page.

  • The *bed.gz files are the source file for the *bb (bigbed) files (i.e. we transformed the bed files to bigbed files using the UCSC bedToBigBed tool - http://hgdownload.cse.ucsc.edu/admin/exe/). Bigbed files can also be transformed back using the bigBedToBed tool.
  • *.tsv.gz files contain both the transformed relative scores and the transformed p-values for TF binding profile matches. Note that their coordinates are 1-based (as opposed to 0-based coordinates used in BED files).
  • To download all files at the same time, use a tool like rsync or wget.

Genomes

We provide predictions for the following species and genomes:

Organism Genome Assembly
Human hg19, hg38
Mus musculus mm10
Danio rerio danRer10
Drosophila melanogaster dm6
Caenorhabditis elegans ce10
Arabidopsis thaliana araTha1
Saccharomyces cerevisiae sacCer3

Citation

A Khan, O Fornes, A Stigliani, A Bessy, M Gheorghe, R van der Lee, J A Castro-Mondragon, J Cheneby, S R Kulkarni, G Tan, D Baranasic, D J Arenillas, A Sandelin, K Vandepoele, B Lenhard, B Ballester, W W Wasserman, F Parcy, A Mathelier. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research. 2018. PMID 29140473


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