κMicroarray analysis of relative gene expression stability for selection of internal reference genes in the rhesus macaque brain

BMC Molecular Biology

Volumn 11, Issue , 2010, Pages

  Noriega, Nigel C ^d   Kohama, Steven G ^a   Urbanski, Henryk F ^a,b,c  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; ACTIN GAMMA 1; ASPARAGINE LINKED GLYCOSYLATION 9 HOMOLOG PROTEIN; CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE II; GENE PRODUCT; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; RIBOSOMAL PROTEIN S27A; RIBOSOME PROTEIN; SEX HORMONE; UBIQUITIN; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN REGION; COMPUTER PROGRAM; CONTROLLED STUDY; FEMALE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC SELECTION; HORMONE SUBSTITUTION; HOUSEKEEPING GENE; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RHESUS MONKEY; SEQUENCE ANALYSIS; ALGORITHM; ANIMAL; BRAIN; GENE EXPRESSION; GENETICS; HISTOLOGY; HUMAN; MACACA MULATTA; MENSTRUATION; METHODOLOGY; PHYSIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARD;

ANIMALIA; MACACA MULATTA;

ALGORITHMS; ANIMALS; BRAIN; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HORMONE REPLACEMENT THERAPY; HUMANS; MACACA MULATTA; MENSTRUATION; MICROARRAY ANALYSIS; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 77953667193     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-11-47     Document Type: Article

References (55)

1. Gibson UE, Heid CA, Williams PM. A novel method for real time quantitative RT-PCR. Genome Res 1996, 6:995-1001. 10.1101/gr.6.10.995, 8908519.
2. Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res 1996, 6:986-994. 10.1101/gr.6.10.986, 8908518.
3. Mutch DM, Berger A, Mansourian R, Rytz A, Roberts MA. Microarray data analysis: a practical approach for selecting differentially expressed genes. Genome Biol 2001, 2:preprint0009.0001-0009.0029.
4. Mutch DM, Berger A, Mansourian R, Rytz A, Roberts MA. The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data. BMC Bioinformatics 2002, 3:17. 10.1186/1471-2105-3-17, 117238, 12095422.
5. Wurmbach E, Yuen T, Sealfon SC. Focused microarray analysis. Methods 2003, 31:306-316. 10.1016/S1046-2023(03)00161-0, 14597315.
6. Provenzano M, Mocellin S. Complementary techniques: validation of gene expression data by quantitative real time PCR. Adv Exp Med Biol 2007, 593:66-73. full_text, 17265717.
7. Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 2004, 15:155-166. 2291693, 15331581.
8. Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 2005, 6:279-284. 10.1038/sj.gene.6364190, 15815687.
9. Tanaka S, Furukawa T, Plotkin SA. Human cytomegalovirus stimulates host cell RNA synthesis. J Virol 1975, 15:297-304. 354453, 163357.
10. Raff T, van der Giet M, Endemann D, Wiederholt T, Paul M. Design and testing of beta-actin primers for RT-PCR that do not co-amplify processed pseudogenes. Biotechniques 1997, 23:456-460.
11. Zhong H, Simons JW. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem Biophys Res Commun 1999, 259:523-526. 10.1006/bbrc.1999.0815, 10364451.
12. Goidin D, Mamessier A, Staquet MJ, Schmitt D, Berthier-Vergnes O. Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Anal Biochem 2001, 295:17-21. 10.1006/abio.2001.5171, 11476540.
13. Zhu G, Chang Y, Zuo J, Dong X, Zhang M, Hu G, Fang F. Fudenine, a C-terminal truncated rat homologue of mouse prominin, is blood glucose-regulated and can up-regulate the expression of GAPDH. Biochem Biophys Res Commun 2001, 281:951-956. 10.1006/bbrc.2001.4439, 11237753.
14. Selvey S, Thompson EW, Matthaei K, Lea RA, Irving MG, Griffiths LR. Beta-actin--an unsuitable internal control for RT-PCR. Mol Cell Probes 2001, 15:307-311. 10.1006/mcpr.2001.0376, 11735303.
15. Glare EM, Divjak M, Bailey MJ, Walters EH. beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax 2002, 57:765-770. 10.1136/thorax.57.9.765, 1746418, 12200519.
16. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, Zumla A. Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 2004, 37:112-114, 116, 118-119.
17. Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem 2005, 344:141-143. 10.1016/j.ab.2005.05.022, 16054107.
18. Sellars MJ, Vuocolo T, Leeton LA, Coman GJ, Degnan BM, Preston NP. Real-time RT-PCR quantification of Kuruma shrimp transcripts: a comparison of relative and absolute quantification procedures. J Biotechnol 2007, 129:391-399. 10.1016/j.jbiotec.2007.01.029, 17350129.
19. Folkersen L, Kurtovic S, Razuvaev A, Agardh HE, Gabrielsen A, Paulsson-Berne G. Endogenous control genes in complex vascular tissue samples. BMC Genomics 2009, 10:516. 10.1186/1471-2164-10-516, 2779820, 19900295.
20. Hoerndli FJ, Toigo M, Schild A, Gotz J, Day PJ. Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction. Anal Biochem 2004, 335:30-41. 10.1016/j.ab.2004.08.028, 15519568.
21. Nieto PA, Covarrubias PC, Jedlicki E, Holmes DS, Quatrini R. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol Biol 2009, 10:63. 10.1186/1471-2199-10-63, 2713239, 19555508.
22. Popovici V, Goldstein DR, Antonov J, Jaggi R, Delorenzi M, Wirapati P. Selecting control genes for RT-QPCR using public microarray data. BMC Bioinformatics 2009, 10:42. 10.1186/1471-2105-10-42, 2640357, 19187545.
23. Stamova BS, Apperson M, Walker WL, Tian Y, Xu H, Adamczy P, Zhan X, Liu DZ, Ander BP, Liao IH, et al. 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.
24. Walker CG, Meier S, Mitchell MD, Roche JR, Littlejohn M. Evaluation of real-time PCR endogenous control genes for analysis of gene expression in bovine endometrium. BMC Mol Biol 2009, 10:100. 10.1186/1471-2199-10-100, 2774697, 19878604.
25. Ahn K, Huh JW, Park SJ, Kim DS, Ha HS, Kim YJ, Lee JR, Chang KT, Kim HS. Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues. BMC Mol Biol 2008, 9:78. 10.1186/1471-2199-9-78, 2561044, 18782457.
26. Noriega NC, Eghlidi DH, Garyfallou VT, Kohama SG, Kryger SG, Urbanski HF. Influence of 17beta-estradiol and progesterone on GABAergic gene expression in the arcuate nucleus, amygdala and hippocampus of the rhesus macaque. Brain Res 2010, 1307:28-42. 10.1016/j.brainres.2009.10.011, 19833106.
27. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
28. Boes T, Neuhauser M. Normalization for Affymetrix GeneChips. Methods Inf Med 2005, 44:414-417.
29. Affymetrix Affymetrix Expression Console™ Software Version 1.0 -- User Guide. 2006, Affymetrix.
30. geNorm Software. , http://medgen.ugent.be/~jvdesomp/genorm/
31. NormFinder Software. , http://www.mdl.dk/publicationsnormfinder.htm
32. BestKeeper software. , http://gene-quantification.com/bestkeeper.html
33. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19:362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
34. 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 Biol 2002, 3:research0034.0031-0034.0011.
35. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
36. Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22:789-794. 10.1093/bioinformatics/btk046, 16410320.
37. Andersen CL, Jensen JL, 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 Res 2004, 64:5245-5250. 10.1158/0008-5472.CAN-04-0496, 15289330.
38. Rasmussen R. Quantification on the LightCycler instrument. Rapid Cycle Real-Time PCR: Methods and Applications 2001, 21-34. Heidelberg: Springer-Verlag Press, Meuer S, Wittwer C, Nakgawara K.
39. Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics 2002, 18:1585-1592. 10.1093/bioinformatics/18.12.1585, 12490442.
40. Urbanski HF, Noriega NC, Lemos DR, Kohama SG. Gene expression profiling in the rhesus macaque: experimental design considerations. Methods 2009, 49:26-31. 10.1016/j.ymeth.2009.05.009, 19467336.
41. Cui X, Loraine AE. Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS ONE 2009, 4:e4229. 10.1371/journal.pone.0004229, 2621337, 19165320.
42. D'Mello V, Lee JY, MacDonald CC, Tian B. Alternative mRNA polyadenylation can potentially affect detection of gene expression by affymetrix genechip arrays. Appl Bioinformatics 2006, 5:249-253. 10.2165/00822942-200605040-00007, 17140271.
43. McClintick JN, Edenberg HJ. Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics 2006, 7:49. 10.1186/1471-2105-7-49, 1409797, 16448562.
44. Noriega NC, Kohama SG, Urbanski HF. Gene expression profiling in the rhesus macaque: methodology, annotation and data interpretation. Methods 2009, 49:42-49. 10.1016/j.ymeth.2009.05.008, 19467334.
45. Cui X, Loraine A. Global correlation analysis between redundant probe sets using a large collection of Arabidopsis ath1 expression profiling data. Comput Syst Bioinformatics Conf 2006:223-226.
46. Stalteri MA, Harrison AP. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 2007, 8:13. 10.1186/1471-2105-8-13, 1784106, 17224057.
47. Spindel ER, Pauley MA, Jia Y, Gravett C, Thompson SL, Boyle NF, Ojeda SR, Norgren RB. Leveraging human genomic information to identify nonhuman primate sequences for expression array development. BMC Genomics 2005, 6:160. 10.1186/1471-2164-6-160, 1314899, 16288651.
48. Tay SK, Blythe J, Lipovich L. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci USA 2009, 106:12019-12024. 10.1073/pnas.0904569106, 2715485, 19581580.
49. Karssen AM, Her S, Li JZ, Patel PD, Meng F, Bunney WE, Jones EG, Watson SJ, Akil H, Myers RM, et al. Stress-induced changes in primate prefrontal profiles of gene expression. Mol Psychiatry 2007, 12:1089-1102. 10.1038/sj.mp.4002095, 17893703.
50. Larionov A, Krause A, Miller W. A standard curve based method for relative real time PCR data processing. BMC Bioinformatics 2005, 6:62. 10.1186/1471-2105-6-62, 1274258, 15780134.
51. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations. Biotechnol Lett 2004, 26:509-515. 10.1023/B:BILE.0000019559.84305.47, 15127793.
52. Noriega NC, Garyfallou VT, Kohama SG, Urbanski HF. Glutamate receptor subunit expression in the rhesus macaque locus coeruleus. Brain Res 2007, 1173:53-65. 10.1016/j.brainres.2007.08.007, 2067256, 17765206.
53. NCBI reference sequence (RefSeq): Definitions: Accession Format. , http://www.ncbi.nlm.nih.gov/RefSeq/key.html#accessions
54. Array Design for the GeneChip® Human Genome U133 Set.
55. Technical Note: Design and Performance of the GeneChip® Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Arrays.