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PMID: 15287981 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Statistical modeling for selecting housekeeper genes.

Genome biology ·Vol. 5 ·No. 8 ·2004-00-00 ·Pages R59

Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS

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.

MeSH Terms

ATPases Associated with Diverse Cellular Activities Adenosine Triphosphatases/genetics Algorithms Breast/metabolism Breast Neoplasms/genetics,pathology Cell Line, Tumor DNA, Complementary/genetics DNA-Binding Proteins/genetics Gene Dosage Gene Expression Gene Expression Profiling/methods,standards Genes, Essential/genetics Humans Mitochondrial Proteins Models, Genetic Oligonucleotide Array Sequence Analysis/methods,standards Proteasome Endopeptidase Complex RNA Splicing Factors RNA, Messenger/genetics,metabolism RNA-Binding Proteins/genetics Reference Standards Reverse Transcriptase Polymerase Chain Reaction Ribonucleoprotein, U2 Small Nuclear/genetics Ribosomal Proteins/genetics Transcription Factors/genetics

Chemicals

DNA, Complementary DNA-Binding Proteins MRPL19 protein, human Mitochondrial Proteins PUM1 protein, human RNA Splicing Factors RNA, Messenger RNA-Binding Proteins Ribonucleoprotein, U2 Small Nuclear Ribosomal Proteins SF3A1 protein, human Transcription Factors PSMC4 protein, human Proteasome Endopeptidase Complex Adenosine Triphosphatases ATPases Associated with Diverse Cellular Activities

Authors & Affiliations

7 authors, click to expand affiliations / ORCID

Szabo Aniko

Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA. [email protected]

Perou Charles M

Karaca Mehmet

Perreard Laurent

Palais Robert

Quackenbush John F

Bernard Philip S

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Article Info

Journal

Genome biology

Abbr.

Genome Biol

ISSN

1474-760X

DOI

10.1186/gb-2004-5-8-r59

[email protected]

Published

2004-00-00

Epub

2004-00-29

Pages

R59

Language

English

Region

England

NLM ID

100960660

PMCID

PMC507884

Subset

Grants

NCI NIH HHS · R33 CA097769 · United States

NCI NIH HHS · R33 CA097769-01 · United States

Corrections

ErratumIn

External Links

PubMed source DOI: 10.1186/gb-2004-5-8-r59 PMC Full Text View journal details

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