Expression Stability of Internal Controls: Comparison of 10 Common Markers

• Activity Number: 194
• Type: Contributed
• Date/Time: Tuesday, August 10, 2004 : 8:30 AM to 10:20 AM
• Sponsor: Biometrics Section
• Author(s): Suddhasatta Acharyya*+ and Jyotirmoy Dey
• Companies: Brown University and Schering-Plough Research Institute
• Keywords: internal control ; gene expression ; cancer ; Pittman's test ; SAGE ; microarray

Abstract

Internals controls are markers that are believed to have "stable" expressions in multiple tissue and organ types and are hence useful in validating and normalizing experimental data on other markers that differentially express themselves across tissue types, for example, normal and cancer tissue. We investigate serial analysis of gene expression (SAGE) technique based expression of 10 commonly used internal control to assess their suitability as controls. The 10 markers selected were PPIA, GAPDH, beta-actin, G6PDH, Lamin B1, Cox 4, Aldolase A, Piruvate Kinase, 36B4, and RPL32. All available expression data for these 10 markers in five different organs--brain, breast, prostate, colon, and ovary--were obtained from the National Center for Biotechnology Information web site. For each organ we first compare the expressions of a given marker in bulk tissue (in-vivo) and cell lines (in-vitro). Average expressions for each marker in bulk tissue were then compared across organs using suitable analysis of variance procedures. We then formalize the notion of "stability of expression" of a marker, and for each organ, select the "most stable" among the internal controls on study.