ArticleCell systems2019
Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Emerging insights into enhancer RNAs: biogenesis, function, mechanism, and disease implication.Briefings in bioinformatics · 2026Review
- Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons.bioRxiv : the preprint server for biology · 2025Article
- Learning induces persistent chromatin loops underlying robust gene expression during memory recall.bioRxiv : the preprint server for biology · 2025Article
- Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.Cell genomics · 2024Article
- A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations.bioRxiv : the preprint server for biology · 2024Article
- Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation.bioRxiv : the preprint server for biology · 2023Article
- A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks.Nature communications · 2023Article
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- Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice.Nature communications · 2022Article
- Alteration of genome folding via contact domain boundary insertion.Nature genetics · 2020Article
- 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.Genome biology · 2020Article
- Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression.Nature neuroscience · 2020Article
- HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.Genome biology · 2020Article
- A subset of topologically associating domains fold into mesoscale core-periphery networks.Scientific reports · 2019Article
- 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.Methods (San Diego, Calif.) · 2018Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Chromosome-Conformation-Capture-Carbon-Copy (5C) is a molecular technology based on proximity ligation that enables high-resolution and high-coverage inquiry of long-range looping interactions. Computational pipelines for analyzing 5C data involve a series of interdependent normalization procedures and statistical methods that markedly influence downstream biological results. A detailed analysis of the trade-offs inherent to all stages of 5C data analysis has not been reported. Here, we provide a comparative assessment of method performance at each step in the 5C analysis pipeline, including sequencing depth and library complexity correction, bias mitigation, spatial noise reduction, distance-dependent expected and variance estimation, statistical modeling, and loop detection. We discuss methodological advantages and disadvantages at each step and provide a full suite of algorithms, lib5C, to allow investigators to test the range of approaches on their own 5C data. Principles learned from our comparative analyses can be applied to protein-independent proximity ligation-based data, including Hi-C, 4C, and Capture-C.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.