Washing scaling of GeneChip microarray expression

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Binder, Hans ^a   Krohn, Knut ^b   Burden, Conrad J ^c  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY HOSPITAL LEIPZIG   (Germany)

^c AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CALIBRATION ALGORITHM; CHARACTER OF TARGET; CORRECTION METHOD; EFFECT OF WASHING; MICROARRAY EXPERIMENTS; MICROARRAY EXPRESSIONS; SEQUENCE-SPECIFIC MANNER; STANDARD PROTOCOLS;

CALIBRATION; EXPERIMENTS; MICROARRAYS; PROBES; RATE CONSTANTS;

WASHING;

ALGORITHM; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; KINETICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION;

ALGORITHMS; GENE EXPRESSION PROFILING; KINETICS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 77952701692     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-291     Document Type: Article

References (33)

1. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genetics 1999, 21:20-24.
2. Han T, Melvin C, Shi L, Branham W, Moland C, Pine PS, Thompson K, Fuscoe J. Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions. BMC Bioinformatics 2006, 7(Suppl 2):S17. 10.1186/1471-2105-7-S2-S17, 1683572, 17118138.
3. Pozhitkov AE, Stedtfeld RD, Hashsham SA, Noble PA. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucl Acids Res 2007, 35(9):e70. 10.1093/nar/gkm154, 1888805, 17430966.
4. Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavare S. Explaining differences in saturation levels for Affymetrix GeneChip(R) arrays. Nucl Acids Res 2007, 35(12):4154-4163. 10.1093/nar/gkm348, 1919478, 17567617.
5. Wick L, Rouillard J, Whittam T, Gulari E, Tiedje J, Hashsham S. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucl Acids Res 2006, 34(3):e26. 10.1093/nar/gnj024, 1369288, 16478712.
6. Held G, Grinstein G, Tu Y. Relationship between gene expression and observed intensities in DNA microarrays - a modeling study. Nucl Acids Res 2006, 34(9):e70. 10.1093/nar/gkl122, 1472623, 16723429.
7. Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, Shimizu H, Yomo T. An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 2008, 24(10):1278-1285. 10.1093/bioinformatics/btn109, 2373920, 18378525.
8. Burden CJ. Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed. Physical Biology 2008, 5:016004. 10.1088/1478-3975/5/1/016004, 18369276.
9. Burden C, Pittlekow Y, Wilson S. Adsorption models of hybridisation and post-hybridisation behaviour on oligonucleotide microarrays. Journal of Physics: Condensed Matter 2006, 18:5545-5565.
10. Binder H, Preibisch S. "Hook" calibration of GeneChip-microarrays: Theory and algorithm. Algorithms for Molecular Biology 2008, 3(12).
11. Binder H, Krohn K, Preibisch S. "Hook" calibration of GeneChip-microarrays: chip characteristics and expression measures. Algorithms for Molecular Biology 2008, 3(11).
12. Ikuta S, Takagi K, Bruce Wallace R, K I. Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base pairs. Nucl Acids Res 1987, 15(2):797-811. 10.1093/nar/15.2.797, 340468, 3822815.
13. Halperin A, Buhot A, Zhulina EB. Sensitivity, Specificity, and the Hybridization Isotherms of DNA Chips. Biophys J 2004, 86(2):718-730. 10.1016/S0006-3495(04)74150-8, 1303922, 14747310.
14. Hekstra D, Taussig AR, Magnasco M, Naef F. Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucl Acids Res 2003, 31(7):1962-1968. 10.1093/nar/gkg283, 152799, 12655013.
15. Binder H, Kirsten T, Loeffler M, Stadler P. The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition. J Phys Chem B 2004, 108(46):18003-18014.
16. Burden CJ, Pittelkow YE, Wilson SR. Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays. Stat App in Gen and Mol Biol 2004, 3:35.
17. Gu Q, Sivanandam TM, Kim C. Signal stability of Cy3 and Cy5 on antibody microarrays. Proteome Science 2006, 4(1):21. 10.1186/1477-5956-4-21, 1633729, 17034643.
18. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y. Effects of Atmospheric Ozone on Microarray Data Quality. Anal Chem 2003, 75(17):4672-4675. 10.1021/ac034241b, 14632079.
19. Affymetrix Affymetrix Microarray Suite 5.0. User Guide 2001, Santa Clara, CA: Affymetrix, Inc, Affymetrix.
20. Shi L, Tong W, Su Z, Han T, Han J, Puri R, Fang H, Frueh F, Goodsaid F, Guo L, Branham W, Chen J, Xu ZA, Harris S, Hong H, Xie Q, Perkins R, Fuscoe J. Microarray scanner calibration curves: characteristics and implications. BMC Bioinformatics 2005, 6(Suppl 2):S11. 10.1186/1471-2105-6-S2-S11, 1637029, 16026596.
21. Pozhitkov AE, Boube I, Brouwer MH, Noble PA. Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities. Nucl Acids Res 2010, 38(5):e28. 10.1093/nar/gkp1122, 2836560, 19969547.
22. Sips R. On the structure of a catalyst surface. J Phys Chem 1948, 16:490-499.
23. Affymetrix IVT Labeling Kit TechnicalNote. Technical Note 2004, 1-8. Affymetrix.
24. Guerasimova A, Ivanov I, Lehrach H. A method of one-step enzyme labelling of short oligonucleotide probes for filter hybridisation. Nucl Acids Res 1999, 27(2):703-705. 10.1093/nar/27.2.703, 148235, 9863000.
25. Zhang L, Hurek T, Reinhold-Hurek B. Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations. Nucl Acids Res 2005, 33(19):e166. 10.1093/nar/gni156, 1275592, 16257977.
26. Naef F, Magnasco MO. Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays. Phys Rev E 2003, 68:11906-11910.
27. Binder H, Kirsten T, Loeffler M, Stadler P. Sequence specific sensitivity of oligonucleotide probes. Proceedings of the German Bioinformatics Conference: 2003; Munich 2003, 145-147.
28. Binder H, Preibisch S. Specific and non-specific hybridization of oligonucleotide probes on microarrays. Biophys J 2005, 89:337-352. 10.1529/biophysj.104.055343, 1366534, 15834006.
29. Binder H, Preibisch S, Kirsten T. Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays. Langmuir 2005, 21:9287-9302. 10.1021/la051231s, 16171364.
30. Heim T, Wolterink JK, Carlon E, Barkema GT. Effective affinities in microarray data. J Phys Cond Mat 2006, 18:S525-S536.
31. Binder H, Bruecker J, Burden CJ. Non-specific hybridization scaling of microarray expression estimates - a physico-chemical approach for chip-to-chip normalization. J Phys Chem B 2009, 113:2874-2895. 10.1021/jp808118m, 19708217.
32. Binder H, Preibisch S, Berger H. Calibration of microarray gene-expression data. Methods in Molecular Biology 2009, 375(407). New York: Humana Press, Grützmann R, Pilarski C.
33. Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, Kaplan P, Kulp D, Webster TA. Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci USA 2003, 100(20):11237-11242. 10.1073/pnas.1534744100, 208741, 14500916.