Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores and P values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.     

STIMULATION OF COLLAGEN SYNTHESIS IN RAT CARDIAC FIBROBLASTS BY EXPOSURE TO HYPOXIC CULTURE CONDITIONS AND SUPPRESSION OF THE EFFECT BY NATRIURETIC PEPTIDES

Synthesis of type I and type III collagens by rat cardiac fibroblasts was stimulated when the cells were cultured under 95% N₂/5% CO₂for one hour followed by incubation under normoxic conditions for 24 hours. The stimulative effect was attenutated by the presence of atrial natriuretic peptide (ANP, 10⁻⁶m) or brain natriuretic peptide (BNP, 10⁻⁶m) in the culture medium. Northern blot analysis indicated that α1(I) and α1(III) collagen mRNA levels were also increased by hypoxia, and decreased with the addition of ANP or BNP in a dose-dependent manner. These results indicate interaction between intracellular signals of a physical stimulus (hypoxic stress) and those of a chemical one (ANP or BNP) and demonstrate that both signals regulate collagen synthesis by cardiac fibroblasts at the levels of the mRNAs. The results also suggest that natriuretic peptides produced by cardiomyocytesin vivomay function as paracrine factors that play a role in the prevention of cardiac fibrosis in ischaemic heart diseases.