ArticlePloS one2011
Weighted correlation network analysis (WGCNA) applied to the tomato fruit metabolome.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers, 1 of them a synthesis that pooled it.
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Who cites it
111 citing papers in PubMed, 1 synthesis or guideline pooled it, 222 citations in OpenAlex.
- Identification of key genes in osteosarcoma by meta‑analysis of gene expression microarray.Molecular medicine reports · 2019Pooled it
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- Differentiation of White and Red Galangal Rhizomes by Pseudo-Targeted LC-MS/MS Metabolomics.Chemistry & biodiversity · 2026Article
- Role and mechanisms of moisture regulation in enhancing alfalfa silage quality.BMC plant biology · 2026Article
- Metabolomic Network Analysis Reveals Reorganization of Lipid and Steroid Programs Linked to Right Ventricular-Pulmonary Vascular Function in Pulmonary Hypertension.bioRxiv : the preprint server for biology · 2026Article
- Strigolactone-mediated drought tolerance in maize (Zea mays) seedlings: an omics approach.BMC plant biology · 2026Article
- Transcriptomic and DNA methylation insights into polyploidy-enhanced heat tolerance in rice (Oryza sativa L.).Plant physiology · 2026Article
- Systems analysis of leaf anatomy and transcriptome using unsupervised machine learning provides insight on photosynthesis development and evolution in non-model grasses.Plant direct · 2026Article
- Integrated metabolome and transcriptome reveal the molecular basis of flavonoid pathway-mediated fruit firmness variation in sweet cherry (Current research in food science · 2026Article
- PacBio full-length transcriptome and WGCNA reveal varietal co-expression networks and regulatory dynamics during tea plant (Frontiers in plant science · 2026Article
- Integrated BSA-Seq and WGCNA Analyses Reveal Candidate Genes Associated with Winter Bud Dormancy Maintenance in Fruit Mulberry (Current issues in molecular biology · 2025Article
- Unlocking TB-COPD Pathogenesis: A Biotechnological Approach Targeting the PI3K/Akt Pathway.Iranian journal of biotechnology · 2025Article
- Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients.Amino acids · 2025Article
- Fermented chrysanthemum stem as a source of natural phenolic compounds to alleviate tomato bacterial wilt disease.Horticulture research · 2025Article
- Tetrahymena predation drives adaptive evolution of Salmonella by disrupting O-antigen biosynthesis and upregulating transcriptional regulator csgD.The ISME journal · 2025Article
- Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds.Frontiers in plant science · 2025Article
- A twin analysis to estimate genetic and environmental factors contributing to variation in weighted gene co-expression network module eigengenes.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2025Article
- Exploration of synthesis of anthocyanins in passion fruit pericarp through combinatorial transcriptomic analysis and WGCNA.Frontiers in plant science · 2025Article
- Comparative transcriptome analysis and heterologous overexpression indicate that the ZjZOG gene may positively regulate the size of jujube fruit.BMC plant biology · 2024Article
- Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes.Plant physiology · 2024Article
51 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAdvances in "omics" technologies have revolutionized the collection of biological data. A matching revolution in our understanding of biological systems, however, will only be realized when similar advances are made in informatic analysis of the resulting "big data." Here, we compare the capabilities of three conventional and novel statistical approaches to summarize and decipher the tomato metabolome. METHODOLOGY: Principal component analysis (PCA), batch learning self-organizing maps (BL-SOM) and weighted gene co-expression network analysis (WGCNA) were applied to a multivariate NMR dataset collected from developmentally staged tomato fruits belonging to several genotypes. While PCA and BL-SOM are appropriate and commonly used methods, WGCNA holds several advantages in the analysis of highly multivariate, complex data.
conclusionsPCA separated the two major genetic backgrounds (AC and NC), but provided little further information. Both BL-SOM and WGCNA clustered metabolites by expression, but WGCNA additionally defined "modules" of co-expressed metabolites explicitly and provided additional network statistics that described the systems properties of the tomato metabolic network. Our first application of WGCNA to tomato metabolomics data identified three major modules of metabolites that were associated with ripening-related traits and genetic background.
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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.