3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data

Genome Biol. 2020 Aug 28;21(1):219. doi: 10.1186/s13059-020-02061-9.


An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions.

Keywords: 3D chromatin looping interactions; Chromatin dynamics; Chromosome-conformation-capture; Epigenetics; False discovery rate; Higher-order chromatin architecture.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Benchmarking
  • Chromatin / chemistry*
  • Chromosomes / chemistry*
  • Epigenomics
  • Humans
  • Models, Genetic*
  • Molecular Conformation


  • Chromatin