Selection of control genes for quantitative RT-PCR based on microarray data.

TitleSelection of control genes for quantitative RT-PCR based on microarray data.
Publication TypeJournal Article
Year of Publication2005
AuthorsShulzhenko N, Yambartsev A, Goncalves-Primo A, Gerbase-DeLima M, Morgun A
JournalBiochemical and biophysical research communications
Volume337
Issue1
Pagination306-12
Date Published2005 Nov 11
ISSN0006-291X
KeywordsAlgorithms, Chagas Disease, Data Interpretation, Statistical, Gene Expression Profiling, Graft Rejection, Heart Transplantation, Humans, Myocardium, Oligonucleotide Array Sequence Analysis, Reference Standards, Reverse Transcriptase Polymerase Chain Reaction
Abstract

Use of internal reference gene(s) is necessary for adequate quantification of target gene expression by RT-PCR. Herein, we elaborated a strategy of control gene selection based on microarray data and illustrated it by analyzing endomyocardial biopsies with acute cardiac rejection and infection. Using order statistics and binomial distribution we evaluated the probability of finding low-varying genes by chance. For analysis, the microarray data were divided into two sample subsets. Among the first 10% of genes with the lowest standard deviations, we found 14 genes common to both subsets. After normalization using two selected genes, high correlation was observed between expression of target genes evaluated by microarray and RT-PCR, and in independent dataset by RT-PCR (r = 0.9, p < 0.001). In conclusion, we showed a simple and reliable strategy of selection and validation of control genes for RT-PCR from microarray data that can be easily applied for different experimental designs and tissues.

DOI10.1016/j.bbrc.2005.09.048
Alternate JournalBiochem. Biophys. Res. Commun.