ArticleNucleic acids research2014
fourSig: a method for determining chromosomal interactions in 4C-Seq data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- fourSynergy: ensemble-based interaction calling on 4C-seq data using gradient-free optimization.BioData mining · 2026Article
- FourC: identifying significant and differential contacts in 1D chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.Nucleic acids research · 2024Article
- Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development.Molecular cell · 2022Article
- seRNA PAM controls skeletal muscle satellite cell proliferation and aging through trans regulation of Timp2 expression synergistically with Ddx5.Aging cell · 2022Article
- Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome.iScience · 2022Article
- Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The role of CTCF in the organization of the centromeric 11p15 imprinted domain interactome.Nucleic acids research · 2021Article
- Molecular and computational approaches to map regulatory elements in 3D chromatin structure.Epigenetics & chromatin · 2021Review
- Application of Chromosome Conformation Capture Method for Detection MYC/TRD Chromosomal Translocation in Leukemia Cell Line.International journal of hematology-oncology and stem cell research · 2020Article
- A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation.Human molecular genetics · 2020Article
- Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner.The EMBO journal · 2020Article
- Benchmarking of 4C-seq pipelines based on real and simulated data.Bioinformatics (Oxford, England) · 2019Article
- Enhancer variants associated with Alzheimer's disease affect gene expression via chromatin looping.BMC medical genomics · 2019Article
- Male-Specific Long Noncoding RNAInternational journal of molecular sciences · 2019Article
- 4See: A Flexible Browser to Explore 4C Data.Frontiers in genetics · 2019Article
- High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq).Journal of visualized experiments : JoVE · 2018Article
- Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys.Genome biology · 2018Article
- Article
- A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression.American journal of human genetics · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates.
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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.