Variation of gene expression in Bacillus subtilis samples of fermentation replicates

Abstract

The application of comprehensive gene expression profiling technologies to compare wild and mutated microorganism samples or to assess molecular differences between various treatments has been widely used. However, little is known about the normal variation of gene expression in microorganisms. In this study, an Agilent customized microarray representing 4,106 genes was used to quantify transcript levels of five-repeated flasks to assess normal variation in Bacillus subtilis gene expression. CV analysis and analysis of variance were employed to investigate the normal variance of genes and the components of variance, respectively. The results showed that above 80% of the total variation was caused by biological variance. For the 12 replicates, 451 of 4,106 genes exhibited variance with CV values over 10%. The functional category enrichment analysis demonstrated that these variable genes were mainly involved in cell type differentiation, cell type localization, cell cycle and DNA processing, and spore or cyst coat. Using power analysis, the minimal biological replicate number for a B. subtilis microarray experiment was determined to be six. The results contribute to the definition of the baseline level of variability in B. subtilis gene expression and emphasize the importance of replicate microarray experiments.

Normal operating range (NOR) in Enchytraeus albidus – Transcriptional responses to control conditions

“…According to Zhou et al (2011) the coefficient of variance (CV) between genes from one dataset to another is useful to assess variation, even when there are large differences in their means. Based on the biological variation in Bacillus subtilis gene expression, Zhou et al (2011) established a CV cut-off of 0.1, defining genes with CV > 0.1 as highly variable.…”

“…Some authors have established a database pinpointing the most variable genes of (their) species of interest, e.g. for mice up to 3.3% of the gene expression was found varying between organs (Pritchard et al, 2001) and for the bacteria Bacillus subtilis 11% of the genes showed high variation between replicates (Zhou et al, 2011). Moreover, in e.g.…”