A toolbox of novel murine house-keeping genes identified by meta-analysis of large scale gene expression profiles

Quantitative and semi-quantitative analysis of gene transcripts requires normalization to RNA-input and/or invariantly expressed house-keeping genes. Currently, only a limited choice of reference genes exists, such as GAPDH1, β-actin, or HPRT, whose transcription levels may be less stable than previously thought. We used the meta-database NC-GED, which we had derived from 1968 published murine expression profiles to identify genes with (i) low inter-tissue expression variability and (ii) great stability over 312 conditions, such as experimental drug treatment, age or differentiation. We identified 276 novel genes with “house-keeping” characteristics, including many genes for ribosomal proteins, and aryl-hydrocarbon receptor-interacting protein. Most genes yielded medium to strong fluorescence intensity on the arrays, a relative measure for their cellular expression. We validated the invariant expression levels of eight of the house-keeper candidates in lymph nodes, thymus, liver, kidney and brain of four different mouse strains. In addition, comparative analysis showed the superiority of multiple over single standardization. Caution against established reference genes is justified. The new panel of reference genes is useful for a flexible selection of reference genes in gene expression studies.