ArticleBMC genomics2017
Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 40 citations in OpenAlex.
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- The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.Biology open · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- Enrichment ofInternational journal of molecular sciences · 2024Article
- Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding.Communications biology · 2024Article
- Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS.Bioinformatics (Oxford, England) · 2024Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin.Genome biology · 2022Article
- Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding.iScience · 2022Article
- Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin.iScience · 2021Article
- Different SP1 binding dynamics at individual genomic loci in human cells.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A universal framework for detectingGenome research · 2021Article
- ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.PLoS computational biology · 2021Article
- Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis.Frontiers in genetics · 2021Article
- Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.Nucleic acids research · 2020Article
- AP-1 imprints a reversible transcriptional programme of senescent cells.Nature cell biology · 2020Article
- TopicNet: a framework for measuring transcriptional regulatory network change.Bioinformatics (Oxford, England) · 2020Article
- Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.Genome biology · 2020Article
- A novelGenome research · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region.
resultsWe present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furthermore, we found that tens of thousands of regulatory regions use multiple modules, a structure that cannot be observed with previous hard clustering based methods. The modules discovered recapitulate many published protein-protein physical interactions, have consistent functional annotations of chromatin states, and uncover context specific co-binding such as gene proximal binding of NFY + FOS + SP and distal binding of NFY + FOS + USF. For certain TFs, the co-binding partners of direct binding (motif present) differs from those of indirect binding (motif absent); the distinct set of co-binding partners can predict whether the TF binds directly or indirectly with up to 95% accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory modules.
conclusionsOur results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of combinatorial binding.
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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.