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Dataset Open Access

Virtual ChIP-seq predictions of binding of 31 transcription factor in Roadmap Epigenomics Project tissues

Mehran Karimzadeh; Michael M. Hoffman

This dataset contains predictions of Virtual ChIP-seq for binding of 31 transcription factors in Roadmap Epigenomics dataset tissues with matched DNase-seq and RNA-seq data.

Tarball contains subfolders for each of the 31 TFs where Virtual ChIP-seq median MCC in validation cell types was > 0.3.

Each subfolder contains gzipped BED files. Each file is named as <Tissue>_<Age>_<TF>_<Accession>_Predictions.bed.gz. Columns correspond to Chromosome, Start, End, <Tissue>_<Age>_<TF>_<Accession>, Posterior probability

You can use the posterior probabilities provided in Virchip_PosteriorCutoffs_V2.0.0.tsv. These are posterior probability cutoffs which maximized MCC in H1-hESC cell type, or are set to 0.4 if there was no ChIP-seq data of that TF in H1-hESC (0.4 is the mode of all optimal posterior probability cutoffs in H1-hESC).

Files (18.5 GB)
Name Size
Virchip_PosteriorCutoffs_V2.0.0.tsv
md5:e669d2301306e1c2a707b85b768bfbd5
513 Bytes Download
virchipPredictions_V2.0.0.tar.gz
md5:dbe3a6e8da30601e0844e3a246b17e77
18.5 GB Download
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