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PubMed · 15287981

Statistical modeling for selecting housekeeper genes.

Aniko Szabo·Charles M Perou·Mehmet Karaca·Laurent Perreard·Robert Palais·John F Quackenbush·Philip S Bernard
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Abstract

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.

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ATPases Associated with Diverse Cellular ActivitiesAdenosine TriphosphatasesAlgorithmsBreastBreast NeoplasmsCell Line, TumorDNA, ComplementaryDNA-Binding ProteinsGene DosageGene ExpressionGene Expression ProfilingGenes, EssentialHumansMitochondrial ProteinsModels, GeneticOligonucleotide Array Sequence AnalysisProteasome Endopeptidase ComplexRNA Splicing FactorsRNA, MessengerRNA-Binding ProteinsReference StandardsReverse Transcriptase Polymerase Chain ReactionRibonucleoprotein, U2 Small NuclearRibosomal ProteinsTranscription FactorsJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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Aniko Szabo, Charles M Perou, Mehmet Karaca, Laurent Perreard, Robert Palais, John F Quackenbush, Philip S Bernard. 2004-07-29. Statistical modeling for selecting housekeeper genes.. https://doi.org/10.1186/gb-2004-5-8-r59

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