ArticleGenome biology2015
3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 25 citations in OpenAlex.
- SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single-Cell Gene Expression.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Transcription factors organize into functional groups on the linear genome and in 3D chromatin.Heliyon · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network.Cell reports methods · 2023Article
- Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology.Computational and structural biotechnology journal · 2023Review
- When 3D genome technology meets viral infection, including SARS-CoV-2.Journal of medical virology · 2022Review
- A Simple Evolutionary Model of Genetic Robustness After Gene Duplication.Journal of molecular evolution · 2022Article
- Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin.iScience · 2021Article
- A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation.Molecular therapy. Nucleic acids · 2021Article
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
- Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data.BMC genomics · 2018Article
- TAD-free analysis of architectural proteins and insulators.Nucleic acids research · 2018Article
- BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions.Nature communications · 2017Article
- Modeling gene regulation from paired expression and chromatin accessibility data.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach.PLoS computational biology · 2017Article
- ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.Nucleic acids research · 2017Article
- Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.Frontiers in genetics · 2017Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
Abstract
Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies. 3CPET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interactions. 3CPET results show biologically significant and accurate predictions when validated against experimental and simulation data.
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