ArticlePLoS computational biology2011
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 103 citations in OpenAlex.
- Article
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- System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks.Frontiers in bioengineering and biotechnology · 2022Article
- Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks.mSystems · 2020Article
- Uncovering the cellular capacity for intensive and specific feedback self-control of the argonautes and MicroRNA targeting activity.Nucleic acids research · 2020Article
- Review
- MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.Scientific reports · 2019Article
- Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood (The Plant cell · 2019Article
- Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors.Frontiers in plant science · 2019Article
- An in-silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration.NPJ systems biology and applications · 2019Article
- An Integrated Regulatory Network Based on Comprehensive Analysis of mRNA Expression, Gene Methylation and Expression of Long Non-coding RNAs (lncRNAs) in Myelodysplastic Syndromes.Frontiers in oncology · 2019Article
- Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.Nucleic acids research · 2018Article
- Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.Cell reports · 2018Article
- A microRNA feedback loop regulates global microRNA abundance during aging.RNA (New York, N.Y.) · 2018Article
- Systematic target function annotation of human transcription factors.BMC biology · 2018Article
- Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research.Progress in retinal and eye research · 2016Review
- An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress inAging · 2016Article
- A Hierarchical Framework for State-Space Matrix Inference and Clustering.The annals of applied statistics · 2016Article
- Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to psychiatric disorders.BMC medical genomics · 2016Article
- Integrative analysis of cancer genes in a functional interactome.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a network framework for analyzing multi-level regulation in higher eukaryotes based on systematic integration of various high-throughput datasets. The network, namely the integrated regulatory network, consists of three major types of regulation: TF→gene, TF→miRNA and miRNA→gene. We identified the target genes and target miRNAs for a set of TFs based on the ChIP-Seq binding profiles, the predicted targets of miRNAs using annotated 3'UTR sequences and conservation information. Making use of the system-wide RNA-Seq profiles, we classified transcription factors into positive and negative regulators and assigned a sign for each regulatory interaction. Other types of edges such as protein-protein interactions and potential intra-regulations between miRNAs based on the embedding of miRNAs in their host genes were further incorporated. We examined the topological structures of the network, including its hierarchical organization and motif enrichment. We found that transcription factors downstream of the hierarchy distinguish themselves by expressing more uniformly at various tissues, have more interacting partners, and are more likely to be essential. We found an over-representation of notable network motifs, including a FFL in which a miRNA cost-effectively shuts down a transcription factor and its target. We used data of C. elegans from the modENCODE project as a primary model to illustrate our framework, but further verified the results using other two data sets. As more and more genome-wide ChIP-Seq and RNA-Seq data becomes available in the near future, our methods of data integration have various potential applications.
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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.