Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis

Applied and Environmental Microbiology

Volumn 74, Issue 10, 2008, Pages 2957-2966

  He, Zhili ^a   Zhou, Jizhong ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; DNA SEQUENCES; MICROARRAYS; OLIGONUCLEOTIDES;

HYBRIDIZATION CONDITIONS; SIGNAL-TO-BACKGROUND RATIO (SBR);

SIGNAL TO NOISE RATIO;

GENOMIC DNA; PRIMER DNA;

BACTERIUM; DNA; EMPIRICAL ANALYSIS; EXPERIMENTAL STUDY; GENE; HYBRIDIZATION; POLYMERASE CHAIN REACTION; SIGNAL-TO-NOISE RATIO;

AMPLICON; ARTICLE; DNA TEMPLATE; GENE PROBE; GENE TARGETING; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; SHEWANELLA ONEIDENSIS; SIGNAL NOISE RATIO; STUDENT T TEST; BACTERIAL GENE; BASE MISPAIRING; DNA MICROARRAY; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; LABORATORY DIAGNOSIS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; SENSITIVITY AND SPECIFICITY; SHEWANELLA; STATISTICS;

SHEWANELLA ONEIDENSIS MR-1;

BASE PAIR MISMATCH; DNA PRIMERS; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; GENE EXPRESSION PROFILING; GENES, BACTERIAL; MICROARRAY ANALYSIS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SENSITIVITY AND SPECIFICITY; SHEWANELLA; STATISTICS AS TOPIC;

EID: 44249085420     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02536-07     Document Type: Article

References (36)

1. Aakra, A., O. L. Nyquist, L. Snipen, T. S. Reiersen, and I. F. Nes. 2007. Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization. Appl. Environ. Microbiol. 73:2207-2217.
2. Basarsky, T., D. Verdnik, D. Willis, and J. Zhai. 2000. An overview of a DNA microarray scanner: design essentials for an integrated acquisition and analysis platform. In M. Schena (ed.), Microarray biochip technology. Eaton Publishing, Natick, MA.
3. Bender, K. S., B. C. B. Yen, C. L. Hemme, Z. Yang, Z. He, Q. He, J. Zhou, K. H. Huang, E. J. Alm, T. C. Hazen, A. P. Arkin, and J. D. Wall. 2007. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 73:5389-5400.
4. Bodrossy, L., and A. Sessitsch. 2004. Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol. 7:245-254.
5. Bodrossy, L., N. Stralis-Pavese, M. Konrad-Köszler, A. Weilharter, T. G. Reichenauer, D. Schöfer, and A. Sessitsch. 2006. mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl. Environ. Microbiol. 72:1672-1676.
6. Brodie, E. L., T. Z. DeSantis, J. P. M. Parker, I. X. Zubietta, Y. M. Iceno, and G. L. Andersen. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl. Acad. Sci. USA 104:299-304.
7. Debouck, C., and P. N. Goodfellow. 1999. DNA microarrays in drug discovery and development. Nat. Genet. 21:48-50.
8. Dziejman, M., E. Balon, D. Boyd, C. M. Fraser, J. F. Heidelberg, and J. J. Mekalanos. 2002. Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99:1556-1561.
9. Gresham, D., D. M. Ruderfer, S. C. Pratt, J. Schacherer, M. J. Dunham, D. Botstein, and L. Kruglyak. 2006. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932-1936.
10. Han, W., B. Liu, B. Cao, L. Beutin, U. Krüger, H. Liu, Y. Li, Y. Liu, L. Feng, and L. Wang. 2007. DNA microarray-based identification of serogroups and virulence gene patterns of Escherichia coli isolates associated with porcine postweaning diarrhea and edema disease. Appl. Environ. Microbiol. 73:4082-4088.
11. He, Z., L. Wu, M. W. Fields, and J. Zhou. 2005. Comparison of microarrays with different probe sizes for monitoring gene expression. Appl. Environ. Microbiol. 71:5154-5162.
12. He, Z., L. Wu, X. Li, M. W. Fields, and J. Zhou. 2005. Empirical establishment of oligonucleotide probe design criteria. Appl. Environ. Microbiol. 71:3753-3760.
13. He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle, and J. Zhou. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J. 1:67-77.
14. Hinchliffe, S. J., K. E. Isherwood, R. A. Stabler, M. B. Prentice, A. Rakin, R. A. Nichols, P. C. Oyston, J. Hinds, R. W. Titball, and B. W. Wren. 2003. Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 13:2018-2029.
15. Hoffman, C. S., and S. Winston. 1987. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267-272.
16. Kim, I. J., H. C. Kang, S. G. Jang, S. A. Ahn, H. J. Yoon, and J. G. Park. 2007. Development and applications of a BRAF oligonucleotide microarray. J. Mol. Diagn. 9:55-63.
17. Liebich, J., C. W. Schadt, S. C. Chong, Z. He, S. K. Rhee, and J. Zhou. 2006. Improvement of oligonucleotide design criteria for the development of functional gene microarrays for environmental applications. Appl. Environ. Microbiol. 72:1688-1691.
18. Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K.-H. Schleifer, and M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064-5081.
19. Loy, A., C. Schulz, S. Lücker, A. Schöpfer-Wendels, K. Stoecker, C. Baranyi, A. Lehner, and M. Wagner. 2005. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales." Appl. Environ. Microbiol. 71:1373-1386.
20. Maynard, C., F. Berthiaume, K. Lemarchand, J. Harel, P. Payment, P. Bayardelle, L. Masson, and R. Brousseau. 2005. Waterborne pathogen detection by use of oligonucleotide-based microarrays. Appl. Environ. Microbiol. 71:8548-8557.
21. Odom, J. M., and J. D. Wall. 1987. Properties of a hydrogen-inhibited mutant of Desulfovibrio desulfuricans ATCC 27774. J. Bacteriol. 169:1335-1337.
22. Quiñones, B., C. T. Parker, J. M. Janda, Jr., W. G. Miller, and R. E. Mandrell. 2007. Detection and genotyping of Arcobacter and Campylobacter isolates from retail chicken samples by use of DNA oligonucleotide arrays. Appl. Environ. Microbiol. 73:3645-3655.
23. Ragoussis, J., and G. Elvidge. 2006. Affymetrix GeneChip system: moving from research to the clinic. Exp. Rev. Mol. Diagn. 6:145-152.
24. 2 and nitrogen deposition. Nature 410:809-812.
25. Rhee, S. K., X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317.
26. Rodionov, D. A., I. Dubchak, A. P. Arkin, E. Alm, and M. S. Gelfand. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Genome Biol. 5:R90.
27. Schena, M. 2003. Microarray analysis. John Wiley & Sons, Inc., Hoboken, NJ.
28. Small, J., D. R. Call, F. J. Brockman, T. M. Straub, and D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67:4708-4716.
29. Taroncher-Oldedburg, G., E. M. Griner, C. A. Francis, and B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69:1159-1171.
30. Tiquia, S. M., L. Wu, S. C. Chong, S. Passovets, D. Xu, Y. Xu, and J. Zhou. 2004. Evaluation of 50-mcr oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 36:664-675.
31. Verdick, D., S. Handran, and S. Pickett. 2002. Key considerations for accurate microarray scanning and image analysis, p. 83-98. In G. Kamberova (ed.), DNA array image analysis: nuts and bolts. DNA Press LLC, Salem, MA.
32. Vora, G. J., C. E. Meador, M. M. Bird, C. A. Bopp, J. D. Andreadis, and D. A. Stenger. 2005. Microarray-based detection of genetic heterogeneity, antimicrobial resistance, and the viable but nonculturable state in human pathogenic Vibrio spp. Proc. Natl. Acad. Sci. USA 102:19109-19114.
33. Wu, L., D. K. Thompson, X. D. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38:6775-6782.
34. Zhou, J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288-294.
35. Zhou, J., M. R. Fries, J. C. Chee-Sanford, and J. M. Tiedje. 1995. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene: description of Azoarcus tolulyticus sp. nov. Int. J. Syst. Bacteriol. 45:500-506.
36. Zhou, S., K. Kassauei, D. J. Cutler, G. C. Kennedy, D. Sidransky, A. Maitra, and J. Califano. 2006. An oligonucleotide microarray for high-throughput sequencing of the mitochondrial genome. J. Mol. Diagn. 8:476-482.