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The R WGCNA package was used to find modules of highly correlated genes and characterize their expression patterns53.
We identified modules of highly coexpressed genes, some of which are restricted to a single lineage but most of which are expressed at variable levels across multiple lineages.
Modulated modularity clustering (MMC; [51]) was used to identify separable modules of highly correlated transcripts.
We found 19 modules of highly co-expressed genes.
Modules of highly interconnected genes were identified using hierarchical clustering and intra-modular connectivity was calculated.
Functionally related proteins are known to act usually in the form of modules of highly interacting proteins.
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This led to the identification of a module of highly interconnected genes.
The main findings of this study are that pleiotropic genes in T-cell-associated diseases formed a module of highly interconnected genes.
Observing an entire module of highly co-expressed genes, each represented by an independent probe, all increasing a mere 1.1 fold adds confidence to this small change.
Our WGCNA analysis groups the genes by topological overlap and develops an undirected network with a module (Brown module) of highly connected genes that is associated with innominate artery atherosclerosis.
The transcription factor C-MYC is central to a module of highly connected binding sites that are related to different epigenetic modifications of the core pluripotency-associated network [ 51].
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