ArticleGenome research2007
An Arabidopsis gene network based on the graphical Gaussian model.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 2 of them syntheses that pooled it.
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Who cites it
122 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens.PloS one · 2012Pooled it
- Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana.BMC systems biology · 2010Pooled it
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.Plant communications · 2024Article
- SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer.Cell reports methods · 2024Article
- A gene network-driven approach to infer novel pathogenicity-associated genes: application tomSystems · 2023Article
- RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks.PLoS computational biology · 2023Article
- Genome-wide identification ofFrontiers in plant science · 2023Article
- Sparse Reduced Rank Huber Regression in High Dimensions.Journal of the American Statistical Association · 2023Article
- Co-Expression Network Analysis of Soybean Transcriptome Identify Hub Genes Under Saline-Alkaline and Water Deficit Stress.Iranian journal of biotechnology · 2022Article
- Rice co-expression network analysis identifies gene modules associated with agronomic traits.Plant physiology · 2022Article
- Modeling dynamic correlation in zero-inflated bivariate count data with applications to single-cell RNA sequencing data.Biometrics · 2022Article
- ThePlant direct · 2022Article
- Microscopic image-based covariation network analysis for actin scaffold-modified insulin signaling.iScience · 2021Article
- Probabilistic Graphical Models Applied to Biological Networks.Advances in experimental medicine and biology · 2021Article
- Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data.BMC genomics · 2020Article
- Trehalose-6-phosphate phosphatase E modulates ABA-controlled root growth and stomatal movement in Arabidopsis.Journal of integrative plant biology · 2020Article
- Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- MyoMiner: explore gene co-expression in normal and pathological muscle.BMC medical genomics · 2020Article
- Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models.The Journal of nutrition · 2020Article
62 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a gene network for the Arabidopsis thaliana transcriptome based on a modified graphical Gaussian model (GGM). Through partial correlation (pcor), GGM infers coregulation patterns between gene pairs conditional on the behavior of other genes. Regularized GGM calculated pcor between gene pairs among approximately 2000 input genes at a time. Regularized GGM coupled with iterative random samplings of genes was expanded into a network that covered the Arabidopsis genome (22,266 genes). This resulted in a network of 18,625 interactions (edges) among 6760 genes (nodes) with high confidence and connections representing approximately 0.01% of all possible edges. When queried for selected genes, locally coherent subnetworks mainly related to metabolic functions, and stress responses emerged. Examples of networks for biochemical pathways, cell wall metabolism, and cold responses are presented. GGM displayed known coregulation pathways as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included.
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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.