Global consensus map of human transcription factor footprints

Vierstra, J. <em>et al.</em> <strong>Global reference mapping of human transcription factor footprints.</strong> <em>Nature</em><strong> </strong>583, 729–736 (2020). https://doi.org/10.1038/s41586-020-2528-x Preprint @ bioRxiv: https://doi.org/10.1101/2020.01.31.927798 <strong>Contact:</strong> Jeff Vierstra ([e-mail]) Genomic DNase I footprinting enables quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin. We combined sampling of &gt;67 billion uniquely mapping DNase I cleavages from &gt;240 human cell types and states to index, with unprecedented accuracy and resolution, human genomic footprints and thereby the sequence elements that encode transcription factor recognition sites. Please see http://vierstra.org/resources/dgf for additional information and a complete set of raw DNase I data for individual datasets. Additionally, raw data can also be accessed via the ENCODE data portal (http://encodeproject.org) using the dataset accessions found in Supplementary Table 1. Code for footprint analysis and tutorials on how to access and manipulate digital genomic footprint data can be found at https://footprint-tools.readthedocs.io/en/latest/. All files herein correspond to human genome build version GRCh38 (UCSC hg38). <strong>Dataset contents:</strong> <strong>Biosample metadata</strong> – Supplementary_Table_1.xlsx <strong>Motif clustering metadata </strong>– Supplementary_Table_2.xlsx <strong>ChIP-seq validation metadata </strong>–<strong> </strong>Supplementary_Table_3.xlsx <strong>Consensus footprint coordinates and assigned motif archetypes</strong><br> TSV file (BED-format) with consensus footprint (posterior probability&gt;0.99) coordinates and overlaps with matches to motif model clusters. The legend file contains column definitions in detail. consensus_footprints_and_motifs_hg38.bed.gz consensus_footprints_and_motifs_legend.txt <strong>Motif archetype matches overlapping consensus footprints</strong><br> TSV file (BED-format) containing the coordinates for clustered motif model matches that overlap consensus footprints collapsed_motifs_overlaping_consensus_footprints.bed.gz collapsed_motifs_overlaping_consensus_footprints_legend.txt <strong>Footprint occupancy matrix of consensus footprints</strong><br> Rows are same order as the consensus footprint file and columns are same order as in the metadata files. consensus_index_matrix_full_hg38.txt.gz (Values are –log(1-posterior)) consensus_index_matrix_binary_hg38.txt.gz (binary occupancy matrix, where footprints with posterior footprint probability &gt;0.99 are considered occupied) <strong>Single nucleotide variants tested for allelic imbalance </strong><br> The legend file contains column definitions in detail. genotypes.vcf.gz - Genotyping and allelic read depth for each biosample (see header for more information) tested_snvs_padj.bed.gz - SNVs tested for imbalance (TSV, BED-format) tested_snvs_padj_legend.txt