Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Molecular Systems Biology

Volumn 5, Issue , 2009, Pages

  Margaritis, Thanasis ^a   Lijnzaad, Philip ^a   Van Leenen, Dik ^a   Bouwmeester, Diane ^a   Kemmeren, Patrick ^a   Van Hooff, Sander R ^a   Holstege, Frank C P ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

DNA microarrays; Fluorescent dye labelling; mRNA expression profiling; Normalization; Two channel

Indexed keywords

DEOXYRIBONUCLEOPROTEIN; DYE; COLORING AGENT;

ARTICLE; BIOLOGICAL MODEL; BIOLOGICAL MONITORING; COMPUTER PROGRAM; DIAGNOSTIC ERROR; DNA MICROARRAY; GENE EXPRESSION; GENE SEQUENCE; HUMAN; HYBRIDIZATION; INTERMETHOD COMPARISON; PRIORITY JOURNAL; ARTIFACT; EPIDEMIOLOGY; GENE; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; STAINING; STANDARD;

ARTIFACTS; BASE SEQUENCE; BIAS (EPIDEMIOLOGY); COLORING AGENTS; GENES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; STAINING AND LABELING;

EID: 66249121702     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2009.21     Document Type: Article

References (19)

1. Chen S. De Vries M. A. Bell S. P. (2007) Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading. Genes Dev 21:2897-2907 (Pubitemid 350133438)
2. Chua G. Morris Q. D. Sopko R. Robinson M. D. Ryan O. Chan E. T. Frey B. J. Andrews B. J. Boone C. Hughes T. R. (2006) Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci USA 103:12045-12050 (Pubitemid 44215808)
3. Cox W. G. Beaudet M. P. Agnew J. Y. Ruth J. L. (2004) Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal Biochem 331:243-254 (Pubitemid 38953074)
4. Dobbin K. K. Kawasaki E. S. Petersen D. W. Simon R. M. (2005) Characterizing dye bias in microarray experiments. Bioinformatics 21:2430-2437 (Pubitemid 40731599)
5. Dombkowski A. A. Thibodeau B. J. Starcevic S. L. Novak R. F. (2004) Genespecific dye bias in microarray reference designs. FEBSLett 560:120-124 (Pubitemid 38264304)
6. Hekstra D. Taussig A. R. Magnasco M. Naef F. (2003) Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res 31:1962-1968 (Pubitemid 36432703)
7. Kelley R. Feizi H. Ideker T. (2008) Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics 24:71-77
8. Lariviere L. Seizl M. Van Wageningen S. Rother S. Van De Pasch L. Feldmann H. Strasser K. Hahn S. Holstege F. C. Cramer P. (2008) Structure-system correlation identifies a gene regulatory Mediator submodule. Genes Dev 22:872-877
9. Martin-Magniette M. L. Aubert J. Cabannes E. Daudin J. J. (2005) Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 21:1995-2000 (Pubitemid 40668037)
10. Naef F. Magnasco M. O. (2003) Solving the riddle of the bright mismatches:labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys 68:011906
11. Quackenbush J. (2002) Microarray data normalization and transformation. Nat Genet 32 (Suppl):496-501 (Pubitemid 35435152)
12. Rosenzweig B. A. Pine P. S. Domon O. E. Morris S. M. Chen J. J. Sistare F. D. (2004) Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ Health Perspect 112:480-487 (Pubitemid 38404559)
13. Schuster E. F. Blanc E. Partridge L. Thornton J. M. (2007) Correcting for sequence biases in present/absent calls. Genome Biol 8:R125
14. Smyth G. K. (2005) Limma: Linear Models for Microarray Data. New York:Springer
15. Tan K. Feizi H. Luo C. Fan S. H. Ravasi T. Ideker T. G. (2008) A systems approach to delineate functions of paralogous transcription factors:role of the Yap family in the DNA damage response. Proc Natl Acad Sci USA 105:2934-2939
16. Tuteja G. Jensen S. T. White P. Kaestner K. H. (2008) Cis-regulatory modules in the mammalian liver:composition depends on strength of Foxa2 consensus site. Nucleic Acids Res 36:4149-4157
17. Yang Y. H. Dudoit S. Luu P. Lin D. M. Peng V. Ngai J. Speed T. P. (2002) Normalization for cDNA microarray data:a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30:e15
18. Young R. A. (2000) Biomedical discovery with DNA arrays. Cell 102:9-15
19. Zhang L. Miles M. F. Aldape K. D. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 21:818-821 (Pubitemid 36791403)