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Published January 10, 2020 | Version 1.1.0
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Global consensus map and dynamics of human transcription factor footprints

  • 1. Altius Institute for Biomedical Sciences

Description

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.

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

  • Consensus_footprints_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 TF recognition sequence matches 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

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 3 and 4).

  • 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)

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

  • Motif_clustering_metadata.xlsx

Contact: Jeff Vierstra (jvierstra@altius.org)

Notes

This work was supported by NHGRI grant U54HG007010.

Files

Consensus_footprints_and_motifs_legend.txt

Files (2.7 GB)

Name Size Download all
md5:2a8cd65dceb96fc0fc3a2a1346c1387a
140.7 MB Download
md5:44616a459d6d6b30162ed85a1fd5355f
925 Bytes Preview Download
md5:15f3da13cd57217af1407e0271251ab6
65.5 MB Download
md5:0ee7b596e3ae34d175ef052edbe21004
1.5 GB Download
md5:ee91206f722cf44d7ccb0d4f7d6a074c
40.6 kB Download
md5:882afc8dce3963aed668e9df1df353d8
1.1 GB Download
md5:39a8a566036f6c0b1d97daca0cbc02b3
143.9 kB Download

Additional details

References

  • Vierstra et al. Global reference mapping and dynamics of human transcription factor footprints. (2020). bioRxiv