Statistical modeling for selecting housekeeper genes.
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.
Szabo
Aniko
A
Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA. aniko.szabo@hci.utah.edu
Perou
Charles M
CM
Karaca
Mehmet
M
Perreard
Laurent
L
Palais
Robert
R
Quackenbush
John F
JF
Bernard
Philip S
PS
D000074183:ATPases Associated with Diverse Cellular Activities; D000251:Adenosine Triphosphatases / Q000235:genetics; D000465:Algorithms; D001940:Breast / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D018076:DNA, Complementary / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D018628:Gene Dosage; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards*; D020043:Genes, Essential / Q000235:genetics; D006801:Humans; D024101:Mitochondrial Proteins; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D046988:Proteasome Endopeptidase Complex; D000072260:RNA Splicing Factors; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
D018076:DNA, Complementary; D004268:DNA-Binding Proteins; C496590:MRPL19 protein, human; D024101:Mitochondrial Proteins; C471242:PUM1 protein, human; D000072260:RNA Splicing Factors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D017413:Ribonucleoprotein, U2 Small Nuclear; D012269:Ribosomal Proteins; C088050:SF3A1 protein, human; D014157:Transcription Factors; C088863:PSMC4 protein, human; D046988:Proteasome Endopeptidase Complex; D000251:Adenosine Triphosphatases; D000074183:ATPases Associated with Diverse Cellular Activities