The impact of quantitative optimization of hybridization conditions on gene expression analysis

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Sykacek, Peter ^a   Kreil, David P ^a   Meadows, Lisa A ^b,c   Auburn, Richard P ^b,c   Fischer, Bettina ^b,c   Russell, Steven ^b,c   Micklem, Gos ^b,c,d  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMOUNT OF INFORMATION; DIFFERENTIAL EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; GENE EXPRESSION ANALYSIS; HYBRIDIZATION CONDITIONS; OBJECTIVE OPTIMIZATION; OLIGONUCLEOTIDE MICROARRAY; TRANSCRIPTION FACTOR EXPRESSION;

CALIBRATION; EXPERIMENTS; GENE EXPRESSION; MICROARRAYS; OLIGONUCLEOTIDES;

OPTIMIZATION;

ANIMAL; ARTICLE; CALIBRATION; COMPUTER PROGRAM; DNA MICROARRAY; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION PROFILING; GENETICS; MALE; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; STATISTICAL MODEL; TEMPERATURE; VALIDATION STUDY;

ANIMALS; CALIBRATION; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION PROFILING; LIKELIHOOD FUNCTIONS; LINEAR MODELS; MALE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TEMPERATURE;

EID: 79952517016     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-73     Document Type: Article

References (53)

1. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467-470. 10.1126/science.270.5235.467, 7569999.
2. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14(13):1675-1680. 10.1038/nbt1296-1675, 9634850.
3. Chambers J, Angulo A, Amaratunga D, Guo H, Jiang Y, Wan JS, Bittner A, Frueh K, Jackson MR, Peterson PA, Erlander MG, Ghazal P. DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J Virol 1999, 73(7):5757-5766. 112636, 10364327.
4. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoe-maker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 2001, 19(4):342-347. 10.1038/86730, 11283592.
5. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 2002, 12(11):1749-1755. 10.1101/gr.362402, 187555, 12421762.
6. Stoughton RB. Applications of DNA microarrays in biology. Annu Rev Biochem 2005, 74:53-82. 10.1146/annurev.biochem.74.082803.133212, 15952881.
7. NCBI Genome Assemblies and Resources. , http://www.ncbi.nlm.nih.gov/genome/
8. Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet 1999, 21(1 Suppl):5-9. 10.1038/4429, 9915493.
9. Kreil DP, Russell RR, Russell S. Microarray Oligonucleotide Probes. Methods Enzymol 2006, 410:73. 10.1016/S0076-6879(06)10004-X, 16938547.
10. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 2002, 30(11):e51. 10.1093/nar/30.11.e51, 117213, 12034852.
11. Barrett JC, Kawasaki ES. Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov Today 2003, 8(3):134-141. 10.1016/S1359-6446(02)02578-3, 12568783.
12. Han T, Melvin CD, Shi L, Branham WS, Moland CL, Pine PS, Thompson KL, Fuscoe JC. 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.
13. Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF. Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 2003, 31(14):4211-4217. 10.1093/nar/gkg476, 167637, 12853639.
14. Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su Z, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong H, Xie Q, Perkins RG, Chen JJ, Casciano DA. Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 2005, 6(Suppl 2):S12. 10.1186/1471-2105-6-S2-S12, 1637032, 16026597.
15. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Loben-hofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Bar-bacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Har-bottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker JW. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24(9):1151-1161. 10.1038/nbt1239, 16964229.
16. Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA, Willey JC, Thierry-Mieg J, Thierry-Mieg D, Setterquist RA, Wilson M, Lucas AB, Novo-radovskaya N, Papallo A, Turpaz Y, Baker SC, Warrington JA, Shi L, Herman D. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol 2006, 24(9):1123-1131. 10.1038/nbt1241, 16964226.
17. Holloway AJ, Oshlack A, Diyagama DS, Bowtell DD, Smyth GK. Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. BMC Bioinformatics 2006, 7:511. 10.1186/1471-2105-7-511, 1664592, 17118209.
18. Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB. Improving comparability between microarray probe signals by thermodynamic intensity correction. Nucleic Acids Res 2007, 35(7):e48. 10.1093/nar/gkl1098, 1874658, 17337437.
19. Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir G, Keles S, Thomson J, Stewart R. A survey of the relationships between oligonu-cleotide properties and hybridization intensities in NimbleGen platform. Nucleic Acids Research 2008, 36(9):2926-2938. 10.1093/nar/gkn133, 2396435, 18385155.
20. Mueckstein U, Leparc GG, Posekany A, Hofacker I, Kreil DP. Hybridization thermodynamics of NimbleGen microarrays. BMC Bioinformatics 2010, 11:35. 10.1186/1471-2105-11-35, 2823707, 20085625.
21. Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
22. Ripley BD. Pattern Recognition and Neural Networks 1996, Cambridge: Cambridge University Press.
23. Spang P, Blanchette C, Zuzana H, Marks JR, Nevins J, West M. Prediction and uncertainty in the analysis of gene expression profiles. In Silico Biol 2002, 2(3):369-381.
24. Lee KE, Sha N, Dougherty RR, Vanucci M, Mallick BK. Gene selection: a Bayesian variable selection approach. Bioinformatics 2003, 19:90-97. 10.1093/bioinformatics/19.1.90, 12499298.
25. Sykacek P, Clarkson R, Print C, Furlong R, Micklem G. Bayesian Modelling of Shared Gene Function. Bioinformatics 2007, 21:1936-1944.
26. Hand DJ. Construction and Assessment of Classsification Rules 1997, New York: John Wiley and Sons.
27. Zweig MH, Campbell G. Receiver-operating characteristic (ROC) plots. Clinical Chemistry 1993, 29:561-577.
28. MacKay DJC. Information Theory, Inference and Learning Algorithms 2003, Cambridge UK: Cambridge University Press.
29. Sykacek P, Furlong R, Micklem G. A Friendly Statistics Package for Microarray Analysis. Bioinformatics 2005, 21:4096-4070., http://bioinformatics.oxfordjournals.org/cgi/reprint/bti663?ijkey=UxcmV7ypaHrMDUN&keytype=ref
30. Wernisch L, Kendall SL, Soneji S, Wietzorrek A, Parish T, Hinds J, Butcher PG, Stoker NG. Analysis of whole-genome microarray replicates using mixed models. Bioinformatics 2003, 19:53-61. 10.1093/bioinformatics/19.1.53, 12499293.
31. Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18(suppl 1):S96-S104.
32. FlyBase, A Database of Drosophila Genes & Genomes. , http://www.ybase.org/
33. The Gene Ontology. , http://www.geneontology.org/
34. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003, 425. 10.1038/nature02046, 14562106.
35. Adryan B, Teichmann SA. FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 2006, 22:1532-1533. 10.1093/bioinformatics/btl143, 16613907.
36. Fisher RA. On the interpretation of χ2 from contingency tables, and the calculation of P. Journal of the Royal Statistical Society 1922, 85:87-94.
37. Mukherjee S, Sykacek P, Roberts S, Gurr S. Gene Ranking Using Bootstrapped P-values. ACM SIGKDD Explorations 2004, 5(2).
38. Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 2006, 103(15):5923-8. 10.1073/pnas.0601231103, 1458674, 16585533.
39. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
40. SantaLucia J J, Hicks D. The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 2004, 33:415-440. 10.1146/annurev.biophys.32.110601.141800, 15139820.
41. Dimitrov RA, Zuker M. Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J 2004, 87:215-226. 10.1529/biophysj.103.020743, 1304344, 15240459.
42. Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 2005, (33 Web Server):W577-581. 10.1093/nar/gki591, 1160267, 15980540.
43. Leparc GG, Tuchler T, Striedner G, Bayer K, Sykacek P, Hofacker IL, Kreil DP. Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res 2009, 37(3):e18. 10.1093/nar/gkn1001, 2647282, 19103659.
44. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005, 6(2):R16. 10.1186/gb-2005-6-2-r16, 551536, 15693945.
45. Irizarry RA, Cope LM, Wu Z. Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol 2006, 7(8):404. 10.1186/gb-2006-7-8-404, 1779590, 16953902.
46. Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol 2009, 10(10):R115. 10.1186/gb-2009-10-10-r115, 2784330, 19835606.
47. Auburn RP, Russell RR, Fischer B, Meadows LA, Sevillano Matilla S, Russell S. SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics 2006, 7:102. 10.1186/1471-2105-7-102, 1456992, 16509966.
48. Buhler J, Ideker T, Haynor D. Dapple: Improved techniques for finding spots on DNA microarrays. Technical Report UWTR 2002-08-05, University of Washington, Seattle, USA 2000,
49. Dapple: Image Analysis Software for DNA Microarrays. , http://www.cs.wustl.edu/~jbuhler/research/dapple/
50. Rocke DM, Durbin B. A model for measurement error for gene expression arrays. J Comput Biol 2001, 8(6):557-569. 10.1089/106652701753307485, 11747612.
51. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18(Suppl 1):S96-104.
52. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 2001, 29:365-371. 10.1038/ng1201-365, 11726920.
53. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acid Research 2002, 30:207-210.