The structure of a gene co-expression network reveals biological functions underlying eQTLs.

TitleThe structure of a gene co-expression network reveals biological functions underlying eQTLs.
Publication TypeJournal Article
Year of Publication2013
AuthorsVilla-Vialaneix, N, Liaubet, L, Laurent, T, Cherel, P, Gamot, A, San Cristobal, M
JournalPLoS One
Volume8
Issue4
Paginatione60045
Date Published2013
ISSN1932-6203
KeywordsCluster Analysis, Computational Biology, Gene Expression Regulation, Gene Regulatory Networks, Humans, Hydrogen-Ion Concentration, Muscles, Phenotype, Quantitative Trait Loci
Abstract

What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes. In this article, a case study was conducted with a mammalian species. It showed that the use of a co-expression network based on partial correlation, combined with a relevant clustering of nodes, leads to an enrichment of biological functions of around 83%. Moreover, the use of a spatial statistics approach allowed us to superimpose additional information related to a phenotype; this lead to highlighting specific genes or gene clusters that are related to the network structure and the phenotype. Three main results are worth noting: first, key genes were highlighted as a potential focus for forthcoming biological experiments; second, a set of biological functions, which support a list of genes under partial eQTL control, was set up by an overview of the global structure of the gene expression network; third, pH was found correlated with gene clusters, and then with related biological functions, as a result of a spatial analysis of the network topology.

DOI10.1371/journal.pone.0060045
Alternate JournalPLoS ONE
PubMed ID23577081
PubMed Central IDPMC3618335