page_title: Gene co-expression network
hierarchical_section_title: Gene co-expression network
caption_attribution_description: English: The direction of edges is overlooked in gene co-expression networks while gene regulatory networks try to find the causality relationship among genes.
context_page_description: A gene co-expression network is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. Having gene expression profiles of a number of genes for several samples or experimental conditions, a gene co-expression network can be constructed by looking for pairs of genes which show a similar expression pattern across samples, since the transcript levels of two co-expressed genes rise and fall together across samples. Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex.
  The direction and type of co-expression relationships are not determined in gene co-expression networks; whereas in a gene regulatory network a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition.
context_section_description: A gene co-expression network (GCN) is an undirected graph, where each node corresponds to a gene, and a pair of nodes is connected with an edge if there is a significant co-expression relationship between them. Having gene expression profiles of a number of genes for several samples or experimental conditions, a gene co-expression network can be constructed by looking for pairs of genes which show a similar expression pattern across samples, since the transcript levels of two co-expressed genes rise and fall together across samples. Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex.
  The direction and type of co-expression relationships are not determined in gene co-expression networks; whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition. Compared to a GRN, a GCN does not attempt to infer the causality relationships between genes and in a GCN the edges represent only a correlation or dependency relationship among genes. Modules or the highly connected subgraphs in gene co-expression networks correspond to clusters of genes that have a similar function or involve in a common biological process which causes many interactions among themselves.
  Gene co-expression networks are usually constructed using datasets generated by high-throughput gene expression profiling technologies such as Microarray or RNA-Seq.
caption: The direction of edges is overlooked in gene co-expression networks. While three genes X, Y and Z are found to be co-expressed, it is not determined whether X activates Y and Y activates Z, or Y activates X and Z, or another gene activates three of them.
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