ArticleGenome research2013
Inferring chromatin-bound protein complexes from genome-wide binding assays.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 41 citations in OpenAlex.
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin.iScience · 2021Article
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- A universal framework for detectingGenome research · 2021Article
- Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.Nucleic acids research · 2020Article
- Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks.BMC bioinformatics · 2020Article
- Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions.BMC biology · 2018Article
- TICA: Transcriptional Interaction and Coregulation Analyzer.Genomics, proteomics & bioinformatics · 2018Article
- A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles.Briefings in bioinformatics · 2018Article
- Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.Genome biology · 2017Article
- Regulatory elements in molecular networks.Wiley interdisciplinary reviews. Systems biology and medicine · 2017Review
- Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.Nucleic acids research · 2017Article
- COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features.Nucleic acids research · 2017Article
- Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding.BMC genomics · 2017Article
- A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors.Nucleic acids research · 2016Article
- ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles.Nucleic acids research · 2016Article
- Modeling co-occupancy of transcription factors using chromatin features.Nucleic acids research · 2016Article
- Get to Understand More from Single-Cells: Current Studies of Microfluidic-Based Techniques for Single-Cell Analysis.International journal of molecular sciences · 2015Review
- Single molecule and single cell epigenomics.Methods (San Diego, Calif.) · 2015Review
- A common set of distinct features that characterize noncoding RNAs across multiple species.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide binding assays can determine where individual transcription factors bind in the genome. However, these factors rarely bind chromatin alone, but instead frequently bind to cis-regulatory elements (CREs) together with other factors thus forming protein complexes. Currently there are no integrative analytical approaches that can predict which complexes are formed on chromatin. Here, we describe a computational methodology to systematically capture protein complexes and infer their impact on gene expression. We applied our method to three human cell types, identified thousands of CREs, inferred known and undescribed complexes recruited to these CREs, and determined the role of the complexes as activators or repressors. Importantly, we found that the predicted complexes have a higher number of physical interactions between their members than expected by chance. Our work provides a mechanism for developing hypotheses about gene regulation via binding partners, and deciphering the interplay between combinatorial binding and gene expression.
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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.