Normalization strategies for mRNA expression data in cartilage research

Osteoarthritis and Cartilage

Volumn 16, Issue 8, 2008, Pages 947-955

  Fundel, K ^a   Haag, J ^b   Gebhard, P M ^b   Zimmer, R ^a   Aigner, T ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Bioinformatics; Biostatistics; Chondrocytes; Gene expression; Housekeeping genes

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ADULT; ARTICLE; ARTICULAR CARTILAGE; CARTILAGE CELL; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION; GENETIC VARIABILITY; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; MEDICAL RESEARCH; OSTEOARTHRITIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; STATISTICAL ANALYSIS; UPREGULATION;

ALGORITHMS; CARTILAGE; CHONDROCYTES; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; GENE EXPRESSION; GENE EXPRESSION PROFILING; OSTEOARTHRITIS; REFERENCE VALUES; RNA, MESSENGER;

EID: 46749092075     PISSN: 10634584     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.joca.2007.12.007     Document Type: Article

References (19)

1. Park T., Yi S.G., Kang S.H., Lee S., Lee Y.S., and Simon R. Evaluation of normalization methods for microarray data. BMC Bioinformatics 4 (2003) 33
2. Quackenbush J. Microarray data normalization and transformation. Nat Genet 32 Suppl (2002) 496-501
3. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24 (2006) 1151-1161
4. Aigner T., Fundel K., Saas J., Gebhard P.M., Haag J., Weiss T., et al. Large-scale gene expression profiling reveals major pathogenetic pathways of osteoarthritic cartilage degeneration. Arthritis Rheum 54 (2006) 3533-3544
5. Mankin H.J., Dorfman H., Lippiello L., and Zarins A. Biochemical and metabolic abnormalities in articular cartilage from osteoarthritic human hips. J Bone Joint Surg 53-A (1971) 523-537
6. Bau B., Gebhard P.M., Haag J., Knorr T., Bartnik E., and Aigner T. Relative messenger RNA expression profiling of collagenases and aggrecanases in human articular chondrocytes in vivo and in vitro. Arthritis Rheum 46 (2002) 2648-2657
7. Causton H.C., Quackenbush J., and Brazma A. Image processing, normalisation and data transformation. Microarray Gene Expression Data Analysis: a Beginner's Guide (2003), Blackwell Publishing, Malden, MA 51-70
8. Draghici S. Data Analysis Tools for DNA Microarrays (2003), CRC Press, Florida
9. Parmigiani G., Garett E.S., Irizarry R.A., and Zeger S.L. The Analysis of Gene Expression Data (2003), Springer, New York
10. Speed T.P. Statistical Analysis of Gene Expression Microarray Data (2003), CRC Press, Florida
11. Zien A., Aigner T., Zimmer R., and Lengauer T. Centralization: a new method for the normalization of gene expression data. Bioinformatics 17 (2001) S323-S331
12. Dudoit S., and Yang Y.H. Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In: Parmigiani G., Garett E.S., Irizarry R.A., and Zeger S.L. (Eds). The Analysis of Gene Expression Data (2003), Springer, New York 73-101
13. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100 (2003) 9440-9445
14. Hoffmann R., Seidl T., and Dugas M. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol 3 (2002)
15. Velculescu V.E., Madden S.L., Zhang L., Lash A.E., Yu J., Rago C., et al. Analysis of human transcriptomes. Nat Genet 23 (1999) 387-388
16. Goldsworthy S.M., Goldsworthy T.L., Sprankle C.S., and Butterworth B.E. Variation in expression of genes used for normalization of Northern blots after induction of cell proliferation. Cell Prolif 26 (1993) 511-518
17. Suzuki T., Higgins P.J., and Crawford D.R. Control selection for RNA quantitation. Biotechniques 29 (2000) 332-337
18. Lee P.D., Sladek R., Greenwood C.M., and Hudson T.J. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12 (2002) 292-297
19. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30 (2002) e15