PCRMs, Predicted cis-Regulatory Modules — home

Predicted cis-regulatory modules and their binding sites

CRMs and transcription factor binding sites predicted from public TF ChIP-seq data for human and mouse. Fruit fly, worm and thale cress are coming soon.

  • Human CRMs (v2) 1,426,947
  • Mouse CRMs (v2) 912,197
  • D. melanogaster CRMs (v1) Coming soon
  • C. elegans CRMs (v1) Coming soon
  • A. thaliana CRMs (v1) Coming soon

How the predictions are made

dePCRM2 on GitHub

PCRMs uses dePCRM2, which predicts CRMs from transcription factor (TF) ChIP-seq data alone, with no histone marks or other epigenetic data. It finds TF motifs that repeatedly occur together across thousands of TF ChIP-seq datasets and links their binding sites into cis-regulatory modules.

  1. Step A: Extend binding peaks

    Each TF ChIP-seq binding peak in every dataset is extended at both ends to 1,000 bp, so nearby sites of cooperating TFs are included.

  2. Step B: Find motifs

    ProSampler finds the motifs in each dataset; each shape is a different motif.

  3. Step C: Find co-occurring pairs

    Pairs of motifs that repeatedly occur together in the same peaks are identified in each dataset.

  4. Step D: Merge into unique motifs

    d1d2d3

    Similar motifs from different datasets are clustered into unique motifs (UMs), each likely bound by one TF or TF family.

  5. Step E: Build interaction networks

    Unique motifs that tend to co-occur are connected, giving a network of cooperating TFs.

  6. Step F: Link adjacent binding sites

    CRMCnon-CRMC

    Binding sites are mapped back to the genome and neighbouring sites are linked into CRM candidates (CRMCs).

  7. Step G: Score and filter

    cutoff

    Each candidate gets an SCRM score and p-value. Candidates that pass the p-value cutoff are the predicted CRMs in PCRMs.

  8. Result: predicted CRMs

    The CRMs that pass the cutoff, with their binding sites, make up the maps in PCRMs.

    Browse the CRM maps

Cite PCRMs

Ni P, Su Z. PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. Database 2022; baac024. doi:10.1093/database/baac024