2008
DOI: 10.1186/1471-2105-9-559
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Abstract: Background: Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sa… Show more

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Cited by 16,629 publications
(16,568 citation statements)
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References 41 publications
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“…Expression values were log 2 transformed, and the WGCNA package 127 in R with signed correlations was used to determine gene coexpression modules with a soft threshold value β of 10 and a treecut value of 0.6. Functional annotation of genes within this module was determined by BLASTP search of protein sequences within this module against the A. thaliana TAIR10 (ref.…”
Section: (Supplementarymentioning
confidence: 99%
“…Expression values were log 2 transformed, and the WGCNA package 127 in R with signed correlations was used to determine gene coexpression modules with a soft threshold value β of 10 and a treecut value of 0.6. Functional annotation of genes within this module was determined by BLASTP search of protein sequences within this module against the A. thaliana TAIR10 (ref.…”
Section: (Supplementarymentioning
confidence: 99%
“…Indeed, transcriptome analysis of lasercaptured dopamine neurons from these mice uncovered alterations in many cellular pathways thought to be implicated in PD [82]. For example, Weighted Gene Co-expression Network Analysis [83] of microarray data revealed that superoxide dismutase 2 and endogenous alpha-synuclein are highly correlated hub genes, driving gene expression alterations involved in synaptic and mitochondrial function. At 4 months of age, Thy1-aSyn mice showed altered gene expression in canonical pathways highly relevant for neuronal function (e.g., signaling in 5' adenosine monophosphate-activated protein kinase (AMPK), apoptosis, axonal guidance, integrin, RhoA, ERK/ MAPK, HIF1alpha, and toll-like receptor); in addition, the Weighted Gene Co-expression Network Analysis reveals alterations in a module comprised of genes involved in Nfe2l2 (also known as Nrf2) oxidative stress response and Dnajc (heat shock protein).…”
Section: Thy1-asyn Mice Show Progressive Molecular Alterations In Mecmentioning
confidence: 99%
“…WGCNA weights the Pearson 'correlation matrix' by taking their absolute value and raising them to the power ß, producing an 'adjacency matrix' (Langfelder and Horvath, 2008). This step emphasizes strong correlations and punishes weak correlations on an exponential scale.…”
Section: Weighted Gene Co-expression Network Analysis and Module Charmentioning
confidence: 99%
“…gene tree of closest pairwise neighbors), and co-expression modules were detected as branches of the gene dendrogram using the hybrid tree-cut algorithm (Fig. S4) (Langfelder and Horvath, 2008). With minimal module size set to 15 probes and merging threshold set to 0.1, 20 modules were detected.…”
Section: Weighted Gene Co-expression Network Analysis and Module Charmentioning
confidence: 99%