ArticleScientific reports2012
Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes.
Article in Scientific reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 27 citations in OpenAlex.
- Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors.Frontiers in plant science · 2019Article
- Constructing tissue-specific transcriptional regulatory networks via a Markov random field.BMC genomics · 2018Article
- Inference of Crosstalk Effects between DNA Methylation and lncRNA Regulation in NSCLC.BioMed research international · 2018Article
- An integrative method to decode regulatory logics in gene transcription.Nature communications · 2017Article
- Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns.Scientific reports · 2017Article
- Genomic feature extraction and comparison based on global alignment of ChIP-sequencing data.Bioengineered · 2017Article
- Article
- COPAR: A ChIP-Seq Optimal Peak Analyzer.BioMed research international · 2017Article
- Network Modularity in Breast Cancer Molecular Subtypes.Frontiers in physiology · 2017Article
- Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment.Molecular endocrinology (Baltimore, Md.) · 2016Article
- Community Structure Reveals Biologically Functional Modules in MEF2C Transcriptional Regulatory Network.Frontiers in physiology · 2016Article
- Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops.The Journal of biological chemistry · 2015Article
- PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.Nucleic acids research · 2014Article
- Navigating the transcriptional roadmap regulating plant secondary cell wall deposition.Frontiers in plant science · 2013Review
- Unraveling regulatory programs for NF-kappaB, p53 and microRNAs in head and neck squamous cell carcinoma.PloS one · 2013Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Recent genome-wide profiling reveals highly complex regulation networks among ERα and its targets. We integrated estrogen (E2)-stimulated time-series ERα ChIP-seq and gene expression data to identify the ERα-centered transcription factor (TF) hubs and their target genes, and inferred the time-variant hierarchical network structures using a Bayesian multivariate modeling approach. With its recurrent motif patterns, we determined three embedded regulatory modules from the ERα core transcriptional network. The GO analyses revealed the distinct biological function associated with each of three embedded modules. The survival analysis showed the genes in each module were able to render a significant survival correlation in breast cancer patient cohorts. In summary, our Bayesian statistical modeling and modularity analysis not only reveals the dynamic properties of the ERα-centered regulatory network and associated distinct biological functions, but also provides a reliable and effective genomic analytical approach for the analysis of dynamic regulatory network for any given TF.
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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.