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

ABSTRACT: 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.

SUBMITTER: Fernandez LR

PROVIDER: S-EPMC7496221 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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

Fernandez Lindsey R LR Gilgenast Thomas G TG Phillips-Cremins Jennifer E JE

Genome biology 20200828 1

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) a ...[more]

PMID: 32859248

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