ArticlePloS one2014
Ensemble-based network aggregation improves the accuracy of gene network reconstruction.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development.BMC genomics · 2025Article
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- Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.PloS one · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
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- Constraint-Based, Score-Based and Hybrid Algorithms to Construct Bayesian Gene Networks in the Bovine Transcriptome.Animals : an open access journal from MDPI · 2022Article
- Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.Tree physiology · 2021Article
- Bioengineering strategies to control epithelial-to-mesenchymal transition for studies of cardiac development and disease.APL bioengineering · 2021Review
- Leaf shape inEcology and evolution · 2020Article
- Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Article
- GeNeCK: a web server for gene network construction and visualization.BMC bioinformatics · 2019Article
- Multilayer Aggregation with Statistical Validation: Application to Investor Networks.Scientific reports · 2018Article
- Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model.Microbial genomics · 2018Article
- Co-expression networks reveal the tissue-specific regulation of transcription and splicing.Genome research · 2017Article
- Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data.Plant physiology · 2017Article
- Enhanced construction of gene regulatory networks using hub gene information.BMC bioinformatics · 2017Article
- DMirNet: Inferring direct microRNA-mRNA association networks.BMC systems biology · 2016Article
- Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data.Scientific reports · 2016Article
- Gene regulatory network inference using fused LASSO on multiple data sets.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Reverse engineering approaches to constructing gene regulatory networks (GRNs) based on genome-wide mRNA expression data have led to significant biological findings, such as the discovery of novel drug targets. However, the reliability of the reconstructed GRNs needs to be improved. Here, we propose an ensemble-based network aggregation approach to improving the accuracy of network topologies constructed from mRNA expression data. To evaluate the performances of different approaches, we created dozens of simulated networks from combinations of gene-set sizes and sample sizes and also tested our methods on three Escherichia coli datasets. We demonstrate that the ensemble-based network aggregation approach can be used to effectively integrate GRNs constructed from different studies - producing more accurate networks. We also apply this approach to building a network from epithelial mesenchymal transition (EMT) signature microarray data and identify hub genes that might be potential drug targets. The R code used to perform all of the analyses is available in an R package entitled "ENA", accessible on CRAN (http://cran.r-project.org/web/packages/ENA/).
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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.