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

Genome Biology

Thomas G. Gilgenast¹  Lindsey R. Fernandez¹  Jennifer E. Phillips-Cremins² 

[1] Department of Bioengineering, University of Pennsylvania, 19104, Philadelphia, PA, USA;Department of Bioengineering, University of Pennsylvania, 19104, Philadelphia, PA, USA;Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, 19104, Philadelphia, PA, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 19104, Philadelphia, PA, USA;

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

DOI  :  10.1186/s13059-020-02061-9

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY