ArticlePloS one2012
Comparing statistical methods for constructing large scale gene networks.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 2 of them syntheses that pooled it.
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Who cites it
98 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Explainable AI: A review of applications to neuroimaging data.Frontiers in neuroscience · 2022Pooled it
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
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- Discovery and validation of a 10-gene predictive signature for response to adjuvant chemotherapy in stage II and III colon cancer.Cell reports. Medicine · 2024Article
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- Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.PLoS computational biology · 2023Article
- SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference.BMC genomics · 2022Article
- Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps.Nature communications · 2022Article
- Transcriptomic profiling of whole blood in 22q11.2 reciprocal copy number variants reveals that cell proportion highly impacts gene expression.Brain, behavior, & immunity - health · 2021Article
- NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning.Genomics, proteomics & bioinformatics · 2021Article
- An ancient, conserved gene regulatory network led to the rise of oral venom systems.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Data Integration Challenges for Machine Learning in Precision Medicine.Frontiers in medicine · 2021Review
- Multidimensional Analyses of Tumor Immune Microenvironment Reveal the Possible Rationality of Immunotherapy and Identify High Immunotherapy Response Subtypes for Renal Papillary Cell Carcinoma.Frontiers in immunology · 2021Article
- Identification of key gene modules and genes in colorectal cancer by co-expression analysis weighted gene co-expression network analysis.Bioscience reports · 2020Article
- Construction, comparison and evolution of networks in life sciences and other disciplines.Journal of the Royal Society, Interface · 2020Article
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- Constructing temporal regulatory cascades in the context of development and cell differentiation.PloS one · 2020Article
- Co-expression clustering across flower development identifies modules for diverse floral forms inPeerJ · 2020Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The gene regulatory network (GRN) reveals the regulatory relationships among genes and can provide a systematic understanding of molecular mechanisms underlying biological processes. The importance of computer simulations in understanding cellular processes is now widely accepted; a variety of algorithms have been developed to study these biological networks. The goal of this study is to provide a comprehensive evaluation and a practical guide to aid in choosing statistical methods for constructing large scale GRNs. Using both simulation studies and a real application in E. coli data, we compare different methods in terms of sensitivity and specificity in identifying the true connections and the hub genes, the ease of use, and computational speed. Our results show that these algorithms performed reasonably well, and each method has its own advantages: (1) GeneNet, WGCNA (Weighted Correlation Network Analysis), and ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks) performed well in constructing the global network structure; (2) GeneNet and SPACE (Sparse PArtial Correlation Estimation) performed well in identifying a few connections with high specificity.
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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.