Identification of Reference Genes by Meta Microarray Analyses.

Citation: Too, IHK, Heng, SSJ, Chan, OYW, Keng, BMH, Chia, CY, Lim, CWX, Leong, WT, Chu, QH, Ang, EJG, Lin, YJ, Ling, MHT. 2013. Identification of Reference Genes by Meta-Microarray Analyses. In Microarrays: Principles, Applications and Technologies. Nova Science Publishers, Inc.

Link to the [Abstract and References].

The expression levels of reference genes used in gene expression studies are assumed to not change under most circumstances. However, a number of studies have demonstrated that genes theoretically assumed to be stably expressed were found to vary under experimental conditions. In addition, previous studies have also reported that stably expressed genes in an organ, may not be stably expressed in other organs or in a different organism, suggesting the need to identify reference genes for each organ and each organism. Due to its ability to analyze the expression of thousands of genes in an experiment, microarrays present a suitable resource for the analysis and identification of reference genes. We present four cases on practical applications of microarrays whereby multiple published microarray data sets were examined to identify suitable reference genes using coefficient of variation (CV) and NormFinder. Our results suggest that microtubule affinity-regulating kinase 3 (MARK3) is a suitable reference gene for mouse liver, 40S ribosomal protein S29 (Rps29) is a suitable reference gene for mouse testes and pancreas, signal peptidase complex subunit 1 (SPCS1) and hydroxyacyl-CoA dehydrogenase beta subunit (HADHB) are suitable reference genes for human lungs, and glucan biosynthesis protein G (mdoG) is a suitable reference gene for Escherichia coli. Further analysis suggests that the identified reference genes are involved in fundamental biochemical processes. This supports the theoretical basis and previous studies that housekeeping genes, on the whole, are generally stably expressed. However, our results also suggest that certain housekeeping genes that are stably expressed in one tissue or one organism may not be stably expressed in different tissues or organisms, supporting the need to identify reference genes for each tissue and organism.