Table 1 Glossary of coexpression network terms
From: Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity
Term | Description |
|---|---|
Modularity | Modularity is the innate property of networks, it has been studied across different scientific disciplines. In this manuscript, we use it only to refer to the functional modularity between cichlid oral and pharyngeal jaws, unless otherwise specified |
Module | A cluster of highly interconnected nodes |
Nodes | Denote genes |
Edges | Denote the connections between genes (nodes). In a weighted network, edges are attributed a “weight” based on the Pearson correlation of gene expression between two genes |
Connectivity | In a weighted network, connectivity of a node is calculated as the sum of the weight of its edges. Thus, it represents how correlated a node is with other nodes in the network |
Adjacency matrix | It is a measure of gene coexpression calculated by the absolute value of the Pearson correlation coefficient of gene expression between genes, raised to a power so the degree distribution fits a small-world network |
Topological overlap matrix (TOM) | Clusters the adjacency matrix with the average linkage hierarchical clustering to incorporate network topological similarity |
Module Eigengene (ME) | Represents the gene expression profile of a module and is defined as the first principal component of a module |
Zsummary | Is a composite statistic based on a permutation test that takes into account the connectivity and density of genes in a module |
Gene significance (GS) | Gene significance is used to incorporate external information into the coexpression network. It is the Pearson correlation between genes in a module and traits of interest (i.e. jaw type or species) |