RefGenes: Identification of reliable and condition specific reference genes for RT-qPCR data normalization

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Hruz, Tomas ^a   Wyss, Markus ^a   Docquier, Mylene ^b   Pfaffl, Michael W ^c   Masanetz, Sabine ^c   Borghi, Lorenzo ^a   Verbrugghe, Phebe ^e   Kalaydjieva, Luba ^e   Bleuler, Stefan ^d   Laule, Oliver ^d   Descombes, Patrick ^b   Gruissem, Wilhelm ^a   Zimmermann, Philip ^a  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d NEBION AG   (Switzerland)

^e UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; DATA ANALYSIS; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC DATABASE; GENETIC STABILITY; GENETIC VARIABILITY; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; POPULATION ABUNDANCE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; RELIABILITY; SPECIES DIFFERENCE; VALIDATION PROCESS; ALGORITHM; ANIMAL; ARABIDOPSIS; BIOLOGY; CATTLE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARD; SWINE; VALIDATION STUDY;

ALGORITHMS; ANIMALS; ARABIDOPSIS; CATTLE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SOFTWARE; SWINE; USER-COMPUTER INTERFACE;

EID: 79953095540     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-156     Document Type: Article

References (34)

1. Cui X, Zhou J, Qiu J, Johnson MR, Mrug M. Validation of Endogenous Internal Real-Time PCR Controls in Renal Tissues. Am J Nephrol 2009, 30:413-417. 10.1159/000235993, 2818397, 19729889.
2. Guenin S, Mauriat M, Pellou J, Van Wuytswinkel O, Bellini C, Gutierrez L. Normalization of qRT-PCRdata: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 2009, 60(2):487-493. 10.1093/jxb/ern305, 19264760.
3. Meller M, Vadachkoria S, Luthy D, Williams M. Evaluation of housekeeping genes in placental comparative expression studies. Placenta 2005, 26:601-607. 10.1016/j.placenta.2004.09.009, 16085039.
4. Svingen T, Spiller CM, Kashimada K, Harley VR, Koop- man P. Identification of suitable normalizing genes for quantitative real-time RT-PCR analysis of gene expression in fetal mouse gonads. Sex Dev 2009, 3:194-204. 10.1159/000228720, 19752599.
5. Zhang X, Ding L, Sandford A. Selection of reference genes for gene expression studies in human neutrophils by real-time PCR. BMC Mol Biol 2005, 6:4. 10.1186/1471-2199-6-4, 551605, 15720708.
6. Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalization: strategies and considerations. Genes and Immunity 2005, 6:279-284. 10.1038/sj.gene.6364190, 15815687.
7. Gutierrez L, Mauriat M, Pelloux J, Bellini C, Wuytswinkel OV. Towards a systematic validation of references in real-time RT-PCR. The Plant Cell 2008, 20:1734-1735. 10.1105/tpc.108.059774, 2518241, 18664615.
8. Andersen C, Ledet-Jensen J, Orntoft T. Normalization of Real-Time quantitative reverse transcription- PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Research 2004, 64:5245-5250. 10.1158/0008-5472.CAN-04-0496, 15289330.
9. Cai J, Deng S, Kumpf S, Lee P, Zagouras P, Ryan A, Gallagher D. Validation of rat reference genes for improved quantitative gene expression analysis using low density arrays. Biotechniques 2007, 42(4):503-511. 10.2144/000112400, 17489238.
10. Fischer M, Skowron M, Berthold F. Reliable transcript quantification by real-time reverse transcript-polymerase chain reaction in primary neuroblastoma using normalization to averaged expression levels of the control genes HPRT1 and SDHA. J Mol Diagnostics 2005, 7:89-96.
11. Szabo A, Perou C, Karaca M, Perreard L, Quackenbush J, Bernard P. Statistical modeling for selecting housekeeper genes. Genome Biology 2004, 5:R59. 10.1186/gb-2004-5-8-r59, 507884, 15287981.
12. Brunner A, Yakovlev I, Strauss S. Validating internal controls for quantitative plant gene expression studies. BMC Plant Biology 2004, 4:14. 10.1186/1471-2229-4-14, 515301, 15317655.
13. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 2002, 3(7):0034.I-0034.II.
14. Lindbjerg Andersen J, Jensen L, Orntoft TF. Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. Cancer Research 2004, 64:5245-5250. 10.1158/0008-5472.CAN-04-0496, 15289330.
15. Pfaffl M, Tichopad A, Prgomet C, Neuvians T. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - Excel-based tool using pair-wise correlations. Biotechnology Letters 2004, 26(509):515.
16. Mar J, Kimura Y, Schroder K, Irvine K, Hayashizaki Y, Suzuki H, Hume D, Quackenbush J. Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics 2009, 10:110. 10.1186/1471-2105-10-110, 2680405, 19374774.
17. Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl M, Shipley G, Vandesompele J, Wittwer C. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry 2009, 55(4):611-622. 10.1373/clinchem.2008.112797, 19246619.
18. Czechowski T, Stiit M, Atlmann T, Udvardi M, Scheible W. Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis. Plant Physiol 2005, 139:5-17. 10.1104/pp.105.063743, 1203353, 16166256.
19. Saviozzi S, Cordero F, Lo Iacono M, Novello S, Scagliotti G, Calogero R. Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer. BMC Cancer 2006, 6:200. 10.1186/1471-2407-6-200, 1557528, 16872493.
20. Hamalainen H, Tubman J, Vikman S, Kyrola T, Ylikoski E, Warrington J, Lahesmaa R. Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Anal Biochem 2001, 299(1):63-70. 10.1006/abio.2001.5369, 11726185.
21. Gabrielsson BG, Olofsson LE, Sjogren A, Jernas M, Elander A, Lonn M, Rudemo M, Carlsson LM. Evaluation of reference genes for studies of gene expression in human adipose tissue. Obes Res 2005, 13:649-652. 10.1038/oby.2005.72, 15897472.
22. Stamova BS, Apperson M, Walker WL, Tian Y, Xu H, Adamczy P, Zhan X, Liu DZ, Ander BP, Liao IH, Gregg JP, Turner RJ, Jickling G, Lit L, Sharp FR. Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood. BMC Med Genomics 2009, 2:49. 10.1186/1755-8794-2-49, 2736983, 19656400.
23. Kwon MJ, Oh E, Lee S, Roh MR, Kim SE, Lee Y, Choi YL, In YH, Park T, Koh SS, Shin YK. Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS ONE 2009, 4:e6162. 10.1371/journal.pone.0006162, 2703796, 19584937.
24. Gur-Dedeoglu B, Konu O, Bozkurt B, Ergul G, Seckin S, Yulug IG. Identification of endogenous reference genes for qRT-PCR analysis in normal matched breast tumor tissues. Oncol Res 2009, 17:353-365. 10.3727/096504009788428460, 19544972.
25. Popovici V, Goldstein DR, Antonov J, Jaggi R, Delorenzi M, Wirapati P. Selecting control genes for RT- QPCR using public microarray data. BMC Bio formatics 2009, 10:42.
26. Pilbrow AP, Ellmers LJ, Black MA, Moravec CS, Sweet WE, Troughton RW, Richards AM, Frampton CM, Cameron VA. Genomic selection of reference genes for real-time PCR in human myocardium. BMC Med Genomics 2008, 1:64. 10.1186/1755-8794-1-64, 2632664, 19114010.
27. Frericks M, Esser C. A toolbox of novel murine house-keeping genes identified by meta-analysis of large scale gene expression profiles. Biochim Biophys Acta 2008, 1779:830-837.
28. Lee S, Jo M, Lee J, Koh S, Kim S. Identification of novel universal housekeeping genes by statistical analysis of microarray data. Biochem Mol Biol 2007, 40(2):226-231.
29. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P. Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes. Adv Bioinform 2008,
30. Millenaar F, Okyere J, May S, van Zanten M, Voesenek L, Peeters A. How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics 2006, 7:137. 10.1186/1471-2105-7-137, 1431565, 16539732.
31. Gentleman R, Carey V, Douglas M, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, sawitzki G, Smith C, Smyth G, Tierney L, Yang Y, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
32. Wilson C, Miller C. Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics 2005, 18:3683-5.
33. Fonjallaz P, Ossipow V, Wanner G, Schibler U. The two PAR leucine zipper proteins, TEF and DBP, display similar circadian and tissue-specific expression, but have different target promoter preferences. EMBO J 1996, 15:351-362. 449950, 8617210.
34. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.