Statistical modeling for selecting housekeeper genes
1 Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
2 Lineberger Comprehensive Cancer Center and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
3 ARUP Laboratories Inc., Salt Lake City, UT 84108, USA
4 Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
Genome Biology 2004, 5:R59 doi:10.1186/gb-2004-5-8-r59Published: 29 July 2004
There is a need for statistical methods to identify genes that have minimal variation in expression across a variety of experimental conditions. These 'housekeeper' genes are widely employed as controls for quantification of test genes using gel analysis and real-time RT-PCR. Using real-time quantitative RT-PCR, we analyzed 80 primary breast tumors for variation in expression of six putative housekeeper genes (MRPL19 (mitochondrial ribosomal protein L19), PSMC4 (proteasome (prosome, macropain) 26S subunit, ATPase, 4), SF3A1 (splicing factor 3a, subunit 1, 120 kDa), PUM1 (pumilio homolog 1 (Drosophila)), ACTB (actin, beta) and GAPD (glyceraldehyde-3-phosphate dehydrogenase)). We present appropriate models for selecting the best housekeepers to normalize quantitative data within a given tissue type (for example, breast cancer) and across different types of tissue samples.