Global consensus map and dynamics of human transcription factor footprints

Data associated with publication "Global reference mapping and dynamics of human transcription factor footprints". https://doi.org/10.1101/2020.01.31.927798

These data describe digital genomic footprints derived from 243 human biosamples.

Please see http://vierstra.org/resources/dgf for additional information and a complete set of raw DNase I data.

Metadata with biosample annotation and ENCODE project accessions in Excel format (Extended Data Table 1):

• Consensus_footprints_metadata.xlsx

Motif clustering metdata in Excel format (Extended Data Table 2):

• Motif_clustering_metadata.xlsx

Raw footprint call within individual datasets at a FDR cutoff of 0.01 (additional levels of FDR thresholding can be made available by request). The following tarball contains 243 BED-formatted files, each corresponding to an individual dataset. (Extended Data File 1).

• Footprints_per_sample.0q01.tar.gz

Tab-delimited files with consensus footprint coordinates and overlaps with matches to motif model clusters in human genome build GRCh38/hg38. The legend file contains column definitions in detail (Extended Data File 2).

• Consensus_footprints_and_motifs_hg38.bed.gz
• Consensus_footprints_and_motifs_legend.txt

BED-formatted file containing the coordinates for clustered motif model matches that overlap consensus footprints (Extended Data File 3)

• Collapsed_motifs_overlaping_consensus_footprints.bed.gz
• Collapsed_motifs_overlaping_consensus_footprints_legend.txt

Footprint occupancy matrix of index footprints (rows) vs. biosamples (columns). Rows are same order as the consensus footprint file and columns are same order as in the metadata files (Extended Data Files 4 and 5).

• Consensus_footprints_and_motifs_matrix_full_hg38.txt.gz (Values are -log(1-posterior))
• Consensus_footprints_and_motifs_matrix_binary_hg38.txt.gz (binary occupancy matrix, where footprints with posterior footprint probability >0.99 are considered occupied)

Single nucleotide variants tested for allelic imbalance. The legend file contains column definitions in detail (Extended Data File 6).

• De_novo_SNVs_tested_for_imbalance.bed.gz
• De_novo_SNVs_tested_for_imbalance.legend.txt

Contact: Jeff Vierstra (jvierstra@altius.org)