Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Su, Li Jen ^a,b   Chang, Ching Wei ^c   Wu, Yu Chung ^b   Chen, Kuang Chi ^d   Lin, Chien Ju ^a   Liang, Shu Ching ^a   Lin, Chi Hung ^e   Whang Peng, Jacqueline ^a   Hsu, Shih Lan ^f   Chen, Chen Hsin ^c,g   Huang, Chi Ying F ^a,e,g  

^a NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^b TAIPEI VETERANS GENERAL HOSPITAL   (Taiwan)

^c INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^d NATIONAL CHUNG CHENG UNIVERSITY   (Taiwan)

^e NATIONAL YANG MING UNIVERSITY   (Taiwan)

^f TAICHUNG VETERANS GENERAL HOSPITAL   (Taiwan)

^g NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DEAD BOX PROTEIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PROTEIN DDX5; RNA; UNCLASSIFIED DRUG; DDX5 PROTEIN, HUMAN;

ARTICLE; BOOTSTRAPPING; CONTROLLED STUDY; DATA ANALYSIS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; INFORMATION PROCESSING; LUNG ADENOCARCINOMA; MICROARRAY ANALYSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SAMPLING; STATISTICAL ANALYSIS; VALIDATION PROCESS; ADENOCARCINOMA; ALGORITHM; CALIBRATION; CELL LINE; COMPARATIVE STUDY; DNA MICROARRAY; EVALUATION; GENE EXPRESSION REGULATION; GENETICS; LABORATORY DIAGNOSIS; LUNG TUMOR; METHODOLOGY; PATHOLOGY; STANDARD;

ADENOCARCINOMA; ALGORITHMS; CALIBRATION; CELL LINE, TRANSFORMED; DATA INTERPRETATION, STATISTICAL; DEAD-BOX RNA HELICASES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECIMEN HANDLING;

EID: 34347209095     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-140     Document Type: Article

References (47)

1. Jain KK Applications of biochips: From diagnostics to personalized medicine Curr Opin Drug Discov Devel 2004 7 3 285-289 15216931
2. Lipshutz RJ Fodor SP Gingeras TR Lockhart DJ High density synthetic oligonucleotide arrays Nat Genet 1999 21 1 Suppl 20-24 10.1038/4447 9915496
3. Bustin SA Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays J Mol Endocrinol 2000 25 2 169-193 10.1677/jme.0.0250169 11013345
4. Yun JJ Heisler LE Hwang Wilkins O Lau SK Hyrcza M Jayabalasingham B Jin J McLaurin J Tsao MS Der SD Genomic DNA functions as a universal external standard in quantitative real-time PCR Nucleic Acids Res 2006 34 12 e85 1524913 16840529 10.1093/nar/gkl400
5. Lee LG Connell CR Bloch W Allelic discrimination by nick-translation PCR with fluorogenic probes Nucleic Acids Res 1993 21 16 3761-3766 309885 8367293 10.1093/nar/21.16.3761
6. Livak KJ Flood SJ Marmaro J Giusti W Deetz K Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization PCR Methods Appl 1995 4 6 357-362 7580930
7. Aerts JL Gonzales MI Topalian SL Selection of appropriate control genes to assess expression of tumor antigens using real-time RT-PCR Biotechniques 2004 36 1 84-6, 88, 90-1 14740490
8. Kim BR Nam HY Kim SU Kim SI Chang YJ Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice Biotechnol Lett 2003 25 21 1869-1872 10.1023/A:1026298032009 14677714
9. Suzuki T Higgins PJ Crawford DR Control selection for RNA quantitation Biotechniques 2000 29 2 332-337 10948434
10. Thellin O Zorzi W Lakaye B De Borman B Coumans B Hennen G Grisar T Igout A Heinen E Housekeeping genes as internal standards: Use and limits J Biotechnol 1999 75 2-3 291-295 10.1016/S0168-1656(99)00163-7 10617337
11. Lin YS Su LJ Yu CT Wong FH Yeh HH Chen SL Wu JC Lin WJ Shiue YL Liu HS Hsu SL Lai JM Huang CY Gene expression profiles of the aurora family kinases Gene Expr 2006 13 1 15-26 16572587
12. Bereta J Bereta M Stimulation of glyceraldehyde-3-phosphate dehydrogenase mRNA levels by endogenous nitric oxide in cytokine-activated endothelium Biochem Biophys Res Commun 1995 217 1 363-369 10.1006/bbrc.1995.2785 8526935
13. Gibbs PJ Cameron C Tan LC Sadek SA Howell WM House keeping genes and gene expression analysis in transplant recipients: A note of caution Transpl Immunol 2003 12 1 89-97 10.1016/S0966-3274(03)00010-8 14551036
14. Hamalainen HK Tubman JC Vikman S Kyrola T Ylikoski E Warrington JA 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
15. 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 7 RESEARCH0034 126239 12184808 10.1186/gb-2002-3-7-research0034
16. Moore DJ Chambers JK Wahlin JP Tan KB Moore GB Jenkins O Emson PC Murdock PR Expression pattern of human P2Y receptor subtypes: A quantitative reverse transcription-polymerase chain reaction study Biochim Biophys Acta 2001 1521 1-3 107-119 11690642
17. Ginzinger DG Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream Exp Hematol 2002 30 6 503-512 10.1016/S0301-472X(02)00806-8 12063017
18. Szabo A Perou CM Karaca M Perreard L Quackenbush JF Bernard PS Statistical modeling for selecting housekeeper genes Genome Biol 2004 5 8 R59 507884 15287981 10.1186/gb-2004-5-8-r59
19. Wilson BJ Bates GJ Nicol SM Gregory DJ Perkins ND Fuller-Pace FV The p68 and p72 DEAD box RNA helicases interact with HDAC1 and repress transcription in a promoter-specific manner BMC Mol Biol 2004 5 11 514542 15298701 10.1186/1471-2199-5-11
20. NetAffx™ Analysis Center https://www.affymetrix.com/site/login/ login.affx
21. geNorm http://medgen.ugent.be/~jvdesomp/genorm
22. Jung M Spthmann J Kalbe A Wankenbauer W Ebenbichler C Jung K Housekeeping gene sets facilitate the search for a suitable reference gene for relative quantification Biochemica 2002 4 9-11
23. Beer DG Kardia SL Huang CC Giordano TJ Levin AM Misek DE Lin L Chen G Gharib TG Thomas DG Lizyness ML Kuick R Hayasaka S Taylor JM Iannettoni MD Orringer MB Hanash S Gene-expression profiles predict survival of patients with lung adenocarcinoma Nat Med 2002 8 8 816-824 12118244
24. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M Loda M Weber G Mark EJ Lander ES Wong W Johnson BE Golub TR Sugarbaker DJ Meyerson M Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proc Natl Acad Sci U S A 2001 98 24 13790-13795 61120 11707567 10.1073/pnas.191502998
25. Ploner A Miller LD Hall P Bergh J Pawitan Y Correlation test to assess low-level processing of high-density oligonucleotide microarray data BMC Bioinformatics 2005 6 1 80 1084343 15799785 10.1186/1471-2105-6-80
26. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc B 1995 57 1 289-300
27. GNF Genome Informatics Applications & Datasets http://wombat.gnf.org/ index.html
28. Stanford Microarray Database http://genome-www5.stanford.edu/
29. Lung Adenocarcinoma http://genome-www.stanford.edu/lung_cancer/adeno/ index.shtml
30. Liver Cancers http://genome-www.stanford.edu/hcc/index.shtml
31. The Human Cell Cycle Data from Hela Cells http://genome-www.stanford.edu/ Human-CellCycle/Hela/
32. Whitfield ML Sherlock G Saldanha AJ Murray JI Ball CA Alexander KE Matese JC Perou CM Hurt MM Brown PO Botstein D Identification of genes periodically expressed in the human cell cycle and their expression in tumors Mol Biol Cell 2002 13 6 1977-2000 117619 12058064 10.1091/ mbc.02-02-0030.
33. Chu YW Yang PC Yang SC Shyu YC Hendrix MJ Wu R Wu CW Selection of invasive and metastatic subpopulations from a human lung adenocarcinoma cell line Am J Respir Cell Mol Biol 1997 17 3 353-360 9308922
34. Chen JJ Peck K Hong TM Yang SC Sher YP Shih JY Wu R Cheng JL Roffler SR Wu CW Yang PC Global analysis of gene expression in invasion by a lung cancer model Cancer Res 2001 61 13 5223-5230 11431363
35. Su LJ Hsu SL Yang JS Tseng HH Huang SF Huang CY Global gene expression profiling of dimethylnitrosamine-induced liver fibrosis: From pathological and biochemical data to microarray analysis Gene Expr 2006 13 2 107-132 17017125
36. Affymetrix Technical Documentation http://www.affymetrix.com/support/ technical/manuals.affx
37. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/
38. Hubbell E Liu WM Mei R Robust estimators for expression analysis Bioinformatics 2002 18 12 1585-1592 10.1093/bioinformatics/18.12.1585 12490442
39. Microarray Suite Software - Support Materials http://www.affymetrix.com/ support/technical/byproduct.affx?product=mas
40. 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 2 249-264 10.1093/biostatistics/4.2.249 12925520
41. Wu Z Irizarry RA Stochastic models inspired by hybridization theory for short oligonucleotide arrays J Comput Biol 2005 12 6 882-893 10.1089/ cmb.2005.12.882 16108723
42. Lehmann EL Nonparametrics: Statistical Methods Based on Ranks San Francisco, Holden-Day, Inc. 1975
43. Contag SA Gostout BS Clayton AC Dixon MH McGovern RM Calhoun ES Comparison of gene expression in squamous cell carcinoma and adenocarcinoma of the uterine cervix Gynecol Oncol 2004 95 3 610-617 10.1016/j.ygyno.2004.08.021 15581972
44. Efron B Bootstrap methods: Another look at the jacknife. Ann Stat, 1979 7 1-26
45. Davison AC Hinkley DV Bootstrap Methods and Their Application. Cambridge University Press. 1997
46. Lahiri SN Resampling Methods for Dependent Data. Springer-Verlag, New York 2003
47. R Development Core Team: R: A language and environment for statistical computing Vienna, Austria, R Foundation for Statistical Computing 2006