DNA microarrays: Experimental issues, data analysis, and application to bacterial systems

Biotechnology Progress

Volumn 20, Issue 5, 2004, Pages 1309-1324

  Dharmadi, Yandi ^a   Gonzalez, Ramon ^a,b  

^a Iowa State University of Science and Technology   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DATA REDUCTION; GENES; METABOLISM; PERTURBATION TECHNIQUES;

GENE EXPRESSION; MICROARRAYS; TRANSCRIPTIONAL RESPONSE;

DNA;

BACTERIA (MICROORGANISMS);

EID: 5444251009     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp0400240     Document Type: Review

References (163)

1. Gupta, P. K.; Roy, R. J.; Prasad, M. DNA chips, microarrays and genomics. Curr. Sci. 1999, 77, 875-884.
2. Wendisch, V. F.; Zimmer, D. P.; Khodursky, A.; Peter, B.; Cozzarelli, N.; Kustu, S. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Anal. Biochem. 2001, 290, 205-213.
3. Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 1995, 270, 467-470.
4. Lockhart, D. J.; Dong, H. L.; Byrne, M. C.; Follettie, M. T.; Gallo, M. V.; Chee, M. S.; Mittmann, M.; Wang, C. W.; Kobayashi, M.; Horton, H.; Brown, E. L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996, 14, 1675-1680.
5. Kane, M. D.; Jatkoe, T. A.; Stumpf, C. R.; Lu, J.; Thomas, J. D.; Madore, S. J. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000, 28, 4552-4557.
6. Barczak, A.; Rodriguez, M. W.; Hanspers, K.; Koth, L. L.; Tai, Y.-C.; Bolstad, B. M.; Speed, T. P.; Erle, D. J. Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 2003, 17, 1775-1785.
7. Rouillard, J. M.; Zuker, M.; Gulari, E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 2003, 31, 3057-3062.
8. Southern, E.; Mir, K.; Shchepinov, M. Molecular interactions on microarrays. Nat. Genet. 1999, 21, 5-9 Suppl. S.
9. Cheung, V. G.; Morley, M.; Aguilar, F.; Massimi, A.; Kucherlapati, R.; Childs, G. Making and reading microarrays. Nat. Genet. 1999, 21, 15-19 Suppl. S.
10. Okamoto, T.; Suzuki, T.; Yamamoto, N. Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat. Biotechnol. 2000, 18, 438-441.
11. Lipshutz, R. J.; Fodor, S. P. A.; Gingeras, T. R.; Lockhart, D. J. High-density synthetic oligonucleotide arrays. Nat. Genet. 1999, 21, 20-24 Suppl. S.
12. Hughes, T. R.; Mao, M.; Jones, A. R.; Burchard, J.; Marton, M. J.; Shannon, K. W.; Lefkowitz, S. M.; Ziman, M.; Schelter, J. M.; Meyer, M. R.; Kobayashi, S.; Davis, C.; Dai, H.; He, Y. D.; Stephaniants, S. B.; Cavet, G.; Walker, W. L.; West, A.; Coffey, E.; Shoemaker, D. D.; Stoughton, R.; Blanchard, A. P.; Friend, S. H.; Linsley, P. S. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 2001, 19, 342-347.
13. Meloni, R.; Khalfallah, O.; Biguet, N. F. DNA microarrays and pharmacogenomics. Pharmacol. Res. 2004, 49, 303-308.
14. Brazma, A.; Hingamp, P.; Quackenbush, J.; Sherlock, G.; Spellman, P.; Stoeckert, C.; Aach, J.; Ansorge, W.; Ball, C. A.; Causton, H. C.; Gaasterland, T.; Glenisson, P.; Holstege, F. C. P.; Kim, I. F.; Markowitz, V.; Matese, J. C.; 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. Nat. Genet. 2001, 29, 365-371.
15. Wei, Y.; Lee, J.-M.; Richmond, C.; Blattner, F. R.; Rafalski, J. A.; LaRossa, R. A. High-density microarray-mediated gene expression profiling of Escherichia coli. J. Bacteriol. 2001, 183, 545-556.
16. Dudley, A. M.; Aach, J.; Steffen, M. A.; Church, G. M. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7554-7559.
17. Helmann, J. D.; Wu, M. F. W.; Kobel, P. A.; Gamo, F. J.; Wilson, M.; Morshedi, M. M.; Navre, M.; Paddon, C. Global transcriptional response of Bacillus subtilis to heat shock. J. Bacteriol. 2001, 183, 7318-7328.
18. Khil, P. P.; Camerini-Otero, R. D. Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 2002, 44, 89-105.
19. Gonzalez, R.; Tao, H.; Shanmugam, K. T.; York, S. W.; Ingram, L. O. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog. 2002, 18, 6-20.
20. Nadon, R.; Shoemaker, J. Statistical issues with microarrays: processing and analysis. Trends Genet. 2002, 18, 265-271.
21. Churchill, G. A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 2002, 32, 490-495 Suppl. S.
22. Kerr, M. K.; Churchill, G. A. Statistical design and the analysis of gene expression microarray data. Genet. Res. 2001, 77, 123-128.
23. Lee, M. T.; Kuo, F. C.; Whitmore, G. A.; Sklar, J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9834-9839.
24. Yang, Y. H.; Speed T. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 2002, 3, 579-588.
25. Knudsen, S. A Biologist's Guide to Analysis of DNA Microarray Data; John Wiley & Sons: New York, 2002.
26. Schulze, A.; Downward, J. Navigating gene expression using microarrays: a technology review. Nat. Cell Biol. 2001, 3, E190-E195.
27. Sterrenburg, E.; Turk, R.; Boer, J. M.; van Ommen, G. B.; den Dunnen, J. T. A common reference for cDNA microarray hybridizations. Nucleic Acids Res. 2002, 30 (21e116).
28. Hedge, P.; Qi, R.; Abernathy, C. G.; Dharap, S.; Gaspard, R.; Hughes, J. E.; Snesrud, E.; Lee, N.; Quackenbush, J. A concise guide to cDNA microarray analysis. BioTechniques 2000, 29, 548-562.
29. Beneš, V.; Muckenthaler, M. Standardization of protocols in cDNA microarray analysis. Trends Biochem. Sci. 2003, 28, 244-249.
30. Talaat, A. M.; Howard, S. T.; Hale IV, W.; Lyons, R.; Garner, H.; Johnston, S. A. Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res. 2002, 30 (21e104).
31. Quackenbush, J. Microarray data normalization and transformation. Nat. Genet. 2002, 32, 496-501 Suppl. S.
32. Irizarry, R. A.; Hobbs, B.; Collin, F.; Beazer-Barclay, Y. D.; Antonellis, K. J.; Scherf, U.; Speed, T. P. Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. Biostatistics 2003, 4, 249-264.
33. Bolstad, B. M.; Irizarry, R. A.; Astrand, M.; Speed, T. P. A comparison of normalization methods for high-density oligonucleotide array data based on bias and variance. Bioinformatics 2003, 19, 185-193.
34. Yang, Y. H.; Dudoit, S.; Luu, P.; Lin, D. M.; Peng, V.; Ngai, J.; Speed, T. P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Adds Res. 2002, 30 (4e15).
35. Yang, H.; Haddad, H.; Tomas, C.; Alsaker, K.; Papoutsakis, E. T. A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1122-1127.
36. Newton, M. A.; Kendziorski, C. M.; Richmond, C. S.; Blattner, F. R.; Tsui, K. W. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol. 2001, 8, 37-52.
37. Kerr, M. K.; Martin, M.; Churchill, G. A. Analysis of variance for gene expression microarray data. J. Comput. Biol. 2000, 7, 819-837.
38. 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, 96S-104S.
39. Wildsmith, S. E.; Archer, G. E.; Winkley, A. J.; Lane, P. W.; Bugelski, P. J. Maximization of signal derived from cDNA microarrays. BioTechniques 2001, 30, 202-208.
40. Electronic Statistics Textbook; StatSoft, Inc.: Tulsa, OK, 2003. WEB: http://www.statsoft.com/textbook/stathome.html.
41. Hochberg, Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 1988, 75, 800-803.
42. Holm, S. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 1979, 6, 65-70.
43. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B-Stat. Methodol. 1995, 57, 289-300.
44. Westfall, P. H.; Young, S. S. Resampling-Based Multiple Testing; Wiley: New York, 1993.
45. Westfall, P. H.; Wolfinger, R. D. Multiple tests with discrete distributions. Am. Stat. 1997, 51, 3-8.
46. Satagopan, J. M.; Panageas, K. S. A statistical perspective on gene expression data analysis. Stat. Med. 2003, 22, 481-499.
47. Kerr, M. K.; Afshari, C. A.; Bennett, L.; Bushel, P.; Martinez, J.; Walker, N. J.; Churchill, G. A. Statistical analysis of a gene expression microarray experiment with replication. Stat. Sin. 2002, 12, 203-217.
48. Slonim, D. K. From patterns to pathways: gene expression data analysis comes of age. Nat. Genet. 2002, 32, 502-08 Suppl. S.
49. Johnsson, R. A.; Wichern, D. W. Applied Multivariate Statistical Analysis; Prentice Hall: Englewood Cliffs, NJ, 1992.
50. Dooley, T. P.; Curto, E. V.; Davis, R. L.; Grammatico, P.; Robinson, E. S.; Wilborn, T. W. DNA microarrays and likelihood ratio bioinformatic methods: discovery of human melanocyte biomarkers. Pigm. Cell Res. 2003, 16, 245-253.
51. Wall, M. E.; Dyck, P. A.; Brettin, T. S. SVDMAN-Singular value decomposition analysis of microarray data. Bioinformatics 2001, 17, 566-568.
52. Fuller, G. N.; Hess, K. R.; Rhee, C. H.; Yung, W. K. A.; Sawaya, R. A.; Bruner, J. M.; Zhang W. Molecular classification of human diffuse gliomas by multidimensional scaling analysis of gene expression profiles parallels morphology-based classification, correlates with survival, and reveals clinically relevant novel glioma subsets. Brain Pathol. 2002, 12, 108-116.
53. Liang, J.; Kachalo, S. Computational analysis of microarray gene expression profiles: clustering, classification, and beyond. Chemom. Intell. Lab. Syst. 2002, 62, 199-216.
54. Yeung, K. Y.; Medvedovic, M.; Bumgarner, R. E. Clustering gene-expression data with repeated measurements. Genome Biol. 2003, 4 (5R34).
55. Kerr, M. K.; Churchill, G. A. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8961-8965.
56. Zhang, K.; Zhao, H. Assessing reliability of gene clusters from gene expression data. Funct. Integr. Genomics 2000, 1, 156-173.
57. Goldstein, D. R.; Ghosh, D.; Conlon, E. M. Statistical issues in the clustering of gene expression data. Stat. Sin. 2002, 12, 219-240.
58. Chen, G. X.; Jaradat, S. A.; Banerjee, N.; Tanaka, T. S.; Ko, M. S. H.; Zhang, M. Q. Evaluation and comparison of clustering algorithms in analyzing ES cell gene expression data. Stat. Sin. 2002, 12, 241-262.
59. McShane, L. M.; Radmacher, M. D.; Freidlin, B.; Yu, R.; Li, M.-C.; Simon, R. Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics 2002, 18, 1462-1469.
60. Tao, H.; Gonzalez, R.; Martinez, A.; Rodriguez, M.; Ingram, L. O.; Preston, J. F.; Shanmugam, K. T. Engineering a homoethanol pathway in Escherichia coli: increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J. Bacteriol. 2001, 183, 2979-2988.
61. Ressom, H.; Wang, D.; Natarajan, P. Adaptive double self-organizing maps for clustering gene expression profiles. Neural Networks 2003, 16, 633-640.
62. Hautaniemi, S.; Yli-Harja, O.; Astola, J.; Kauraniemi, P.; Kallioniemi, A.; Wolf, M.; Ruiz, J.; Mousses, S.; Kallioniemi, O. P. Analysis and visualization of gene expression microarray data in human cancer using self-organizing maps. Mach. Learn. 2003, 52, 45-66.
63. McLachlan, G. J. Discriminant Analysis and Statistical Pattern Recognition; Wiley: New York, 1992.
64. Ripley, B. D. Pattern Recognition and Neural Networks; Cambridge University Press: Cambridge, UK, 1996.
65. Dudoit, S.; Fridlyand, J.; Speed, T. P. Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc. 2002, 97, 77-87.
66. Bura, E.; Pfeiffer, R. M. Graphical methods for class prediction using dimension reduction techniques on DNA microarray data. Bioinformatics 2003, 19, 1252-1258.
67. Ishwaran, H.; Rao, J. S. Detecting differentially expressed genes in microarrays using Bayesian model selection. J. Am. Stat. Assoc. 2003, 98, 438-455.
68. Baldi, P.; Long, A. D. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical snferences of gene changes. Bioinformatics 2001, 17, 509-519.
69. Hatfield, G. W.; Hung, S. P.; Baldi, P. Differential analysis of DNA microarray gene expression data. Mol. Microbiol. 2003, 47, 871-877.
70. Kooperberg, C.; Thomas, G.; Fazzio, J.; Delrow; J.; Toshio, T. Improved background correction for spotted DNA microarrays. J. Comput. Biol. 2002, 9, 55-66.
71. Taniguchi, M.; Miura, K.; Iwao, H.; Yamanaka, S. Quantitative assessment of DNA microarrays-comparison with Northern blot analyses. Genomics 2001, 71, 34-39.
72. Rajeevan, M. S.; Vernon, S. D.; Taysavang, N.; Unger, E. R. Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J. Mol. Diagn. 2001, 3, 26-31.
73. Tusher, V. G.; Tibshirani, R.; Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5116-5121.
74. Chuaqui, R. F.; Bonner, R. F.; Best, C. J. M.; Gillespie, J. W.; Flaig, M. J.; Hewitt, S. M.; Phillips, J. L.; Krizman, D. B.; Tangrea, M. A.; Ahram, M.; Linehan, W. M.; Knezevic, V.; Emmert-Buck, M. R. Post-analysis follow-up and validation ofmicroarray experiments. Nat. Genet. 2002, 32, 509-514 Suppl. S.
75. Laub, M. T.; McAdams, H. H.; Feldblyum, T.; Fraser, C. M.; Shapiro, L. Global analysis of the genetic network controlling a bacterial cell cycle. Science 2000, 290, 2144-2128.
76. Tjaden, B.; Saxena, R. M.; Stolyar, S.; Haynor, D. R.; Kolker, E.; Rosenow, C. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 2002, 30, 3732-3738.
77. Kanesaki, Y.; Suzuki, I.; Allakhverdiev, S. I.; Mikami, K., Murata, N. Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803. Biochem. Biophys. Res. Commun. 2002, 290, 339-348.
78. Rozen, Y.; LaRossa, R. A.; Templeton, L. J.; Smulski, D. R.; Belkin, S. Gene expression analysis of the response by Escherichia coli to seawater. Antonie van Leeuwenhoek 2002, 81, 15-25.
79. Cheung, K. J.; Badarinarayana, V.; Selinger, D. W.; Janse, D.; Church, G. M. A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res. 2003, 13, 206-215.
80. Kaan, T.; Homuth, G.; Mader, U.; Bandow, J.; Schweder, T. Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology 2002, 148, 3441-3455.
81. Stewart, G. R.; Wernisch, L.; Stabler, R.; Mangan, J. A.; Hinds, J.; Laing, K. G.; Young, D. B.; Butcher, P. D. Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology 2002, 48, 3129-3138.
82. Tucker, D. L.; Tucker, N.; Conway, T. Gene expression profiling of the pH response in Escherichia coli. J. Bacteriol. 2002, 184, 6551-6558.
83. Polen, T.; Rittmann, D.; Wendisch, V. F.; Sahm, H. DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl. Environ. Microbiol. 2003, 69, 1759-1774.
84. Zheng, M.; Wang, X.; Templeton, L. J.; Smulski, D. R.; LaRossa, R. A.; Sturz, G. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J. Bacteriol. 2001, 183, 4562-4570.
85. Gmuender, H.; Kuratli, K.; Di Padova, K.; Gray, C. P.; Keck, W.; Evers, S. Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciproflaxin: combined transcription and translation analysis. Genome Res. 2001, 11, 28-42.
86. Smulski, D. R.; Huang, L. X. L.; McCluskey, M. P.; Reeve, M. J. G.; Vollmer, A. C.; Van Dyk, T. K.; LaRossa, R. A. Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12. J. Bacteriol. 2001, 183, 3353-3364.
87. Wilson, W.; DeRisi, J.; Kristensen, H. H.; Imboden, P.; Rane, S.; Brown, P. O.; Schoolnik, G. K. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 12833-12838.
88. James, B. W.; Bacon, J.; Hampshire, T.; Morley, K.; Marsh, P. D. In vitro gene expression dissected: chemostat surgery for Mycobacterium tuberculosis. Comp. Funct. Genomics 2002, 3, 345-347.
89. Betts, J. C.; Lukey, P. T.; Robb, L. C.; McAdam, R. A.; Duncan, K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 2002, 43, 717-731.
90. Ishige, T.; Krause, M.; Bott, M.; Wendisch, V. F.; Sahm, H. The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses. J. Bacteriol. 2003, 185, 4519-4529.
91. Tao, H.; Bausch, C.; Richmond, C.; Blattner, F. R.; Conway, T. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 1999, 181, 6425-6440.
92. Paustian, M. L.; May, B. J.; Kapur, V. Transcriptional response of Pasteurella multocida to nutrient limitation. J. Bacteriol. 2002, 184, 3734-3739.
93. Mader, U.; Homuth, G.; Scharf, C.; Buttner, K.; Bode, R.; Hecker, M. Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability. J. Bacteriol. 2002, 184, 4288-4295.
94. Jarmer, H.; Berka, R.; Knudsen, S.; Saxild, H. H. Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions. FEMS Microbiol. Lett. 2002, 206, 197-200.
95. Ye, R. W.; Tao, W.; Bedzyk, L.; Young, T.; Chen, M.; Li, L. Global gene expression profiles of Bacillus subtilis grown under anaerobic condition. J. Bacteriol. 2000, 182, 4458-4465.
96. Paustian, M. L.; May, B. J.; Kapur, V. Pasteurella multocida gene expression in response to iron limitation. Infect. Immun. 2001, 69, 4109-4115.
97. Paustian, M. L.; May, B. J.; Cao, D. W.; Boley, D.; Kapur, V. Transcriptional response of Pasteurella multocida to defined iron sources. J. Bacteriol. 2002, 184, 6714-6720.
98. Hihara, Y.; Kamei, A.; Kanehisa, M.; Kaplan, A.; Ikeuchi, M. DNA microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell 2001, 13, 793-806.
99. Gill, R. T.; Katsoulakis, E.; Schmitt, W.; Taroncher-Oldenburg, G.; Misra, J.; Stephanopoulos, G. Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp strain PCC 6803. J. Bacteriol. 2002, 184, 3671-3681.
100. Oh, M.-K.; Rohlin, L.; Kao, K. C.; Liao, J. C. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 2002, 277, 13175-13183.
101. Hayashi, M.; Mizoguchi, H.; Shiraishi, N.; Obayashi, M.; Nakagawa, S.; Imai, J.; Watanabe, S.; Ota, T.; Ikeda, M. Transcriptome analysis of acetate metabolism in Corynebacterium glutamicum using a newly developed metabolic array. Biosci. Biotechnol. Biochem. 2002, 66, 1337-1344.
102. Oh, M.-K.; Liao, J. C. Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 2000, 16, 278-286.
103. Campbell, J. W.; Morgan-Kiss, R. M.; Cronan, J. E. A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway. Mol. Microbiol. 2003, 47, 793-805.
104. Chhabra, S. R.; Shockley, K. R.; Conners, S. B.; Scott, K. L.; Wolfinger, R. D.; Kelly, R. M. Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritime. J. Biol. Chem. 2003, 278, 7540-7552.
105. DeLisa, M. P.; Wu, C. F.; Wang, L.; Valdes, J. J.; Bentley, W. E. DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J. Bacteriol. 2001, 183, 5239-5247.
106. Firoved, A. M.; Deretic, V. Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa. J. Bacteriol. 2003, 185, 1071-1081.
107. Whiteley, M.; Bangera, M. G.; Bumgarner, R. E.; Parsek, M. R.; Teitzel, G. M.; Lory, S.; Greenberg, E. P. Gene expression in Pseudomonas aeruginosa biofilms. Nature 2001, 413, 860-864.
108. Schembri, M. A.; Kjaergaard, K.; Klemm, P. Global gene expression in Escherichia coli biofilms. Mol. Microbiol. 2003, 48, 253-267.
109. Hautefor, I.; Hinton, J. C. D. Measurement of bacterial gene expression in vivo. Philos. Trans. R. Soc. London, Ser. B 2000, 355, 601-611.
110. Xu, Q.; Dziejman, M.; Mekalanos, J.J. Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1286-1291.
111. Dietrich, G.; Kurz, S.; Hubner, C.; Aepinus, C.; Theiss, S.; Guckenberger, M.; Panzner, U.; Weber, J.; Frosch, M. Transcriptome analysis of Neisseria meningitidis during infection. J. Bacteriol. 2003, 185, 155-164.
112. Boyce, J. D.; Wilkie, I.; Harper, M.; Paustian, M. L.; Kapur, V.; Adler, B. Genomic scale analysis of Pasteurella multocida gene expression during growth within the natural chicken host. Infect. Immun. 2002, 70, 6871-6879.
113. Grandi, G. Antimicrobial vaccine design using genomics and proteomics. Trends Biotechnol. 2001, 19, 181-188.
114. Israel, D. A.; Salama, N.; Krishna, U.; Rieger, U. M.; Atherton, J. C.; Falkow, S.; Peek, R. M. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14625-14630.
115. Chan, K.; Baker, S.; Kim, C. C.; Detweiler, C. S.; Dougan, G.; Falkow, S. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. J. Bacteriol. 2003, 185, 553-563.
116. McCluskey, J.; Dowson, C. G.; Mitchell, T. J. The use of microarray tehcnology for the analysis of Streptoccocus pneumoniae. Comp. Funct. Genomics 2002, 3, 366-368.
117. Kato-Maeda, M.; Rhee, J. T.; Gingeras, T. R.; Salamon, H.; Drenkow, J.; Smittipat, N.; Small, P. M. Comparing genomes within the species Mycobacterium tuberculosis. Genome Res. 2001, 11, 547-554.
118. Call, D. R.; Brockman, F. J.; Chandler, D. P. Detecting and genotyping Escherichia coli O157: H7 using multiplexed PCR and nucleic acid microarray. Int. J. Food Microbiol. 2001, 67, 71-80.
119. Moxon, R.; Tang, C. Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens. Philos. Trans. R. Soc. London, Ser. B 2000, 355, 643-656.
120. Schoolnik, G. K. Functional and comparative genomics of pathogenic bacteria. Curr. Opin. Microbiol. 2002, 5, 20-26.
121. Fitzgerald, J. R.; Studervant, D. E.; Mackie, S. M.; Gill, S. R.; Musser, J. M. Evolutionary genomics of Staphylococcus aureus: insight into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8821-8826.
122. Fitzgerald, J. R.; Musser, J. M. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 2001, 9, 547-553.
123. Malloff, C. A.; Fernandez, R. C.; Lam, W. L. Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer. J. Mol. Biol. 2001, 312, 1-5.
124. Porwollik, S.; Wong, R. M. Y.; McClelland, M. Evolutionary genomics of Salmonella: gene acquisition revealed by microarray Analysis. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 8956-8961.
125. Sabatti, C.; Rohlin, L.; Oh, M.-K; Liao, J. C. Coexpression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res. 2002, 30, 2886-2893.
126. Kendall, S. L.; Movahedzadeh, F.; Wietzorrek, A.; Stoker, N. G. Microarray analysis of bacterial gene expression: towards the regulome. Comp. Funct. Genomics 2002, 3, 352-354.
127. Gaballa, A.; Wang, T.; Ye, R. W.; Helmann, J. D. Functional analysis of the Bacillus subtilis zur regulon. J. Bacteriol. 2002, 184, 6508-65014.
128. Baichoo, N.; Wang, T.; Ye, R.; Helmann, J. D. Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulus. Mol. Microbiol. 2002, 45, 1613-1629.
129. Khodursky, A. B.; Peter, B. J.; Schmidt, M. B.; DeRisi, J.; Botstein, D.; Brown, P. O.; Cozzarelli, N. R. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9419-9424.
130. Bernstein, J. A.; Khodursky, A. B.; Lin, P. H.; Lin-Chao, S.; Cohen, S. N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9697-9702.
131. Britton, P. A.; Eichenberger, P.; Gonzalez-Pastor, J. E.; Fawcett, P.; Monson, R.; Losick, R.; Grossman, A. D. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J. Bacteriol. 2002, 184, 4881-4890.
132. Manganelli, R.; Voskuil, M. I.; Schoolnik, G. K.; Dubnau, E.; Gomez, M.; Smith, I. Role of extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression. Mol. Microbiol. 2002, 45, 365-374.
133. Sebert, M. E.; Palmer, L. M.; Rosenberg, M.; Weiser, J. N. Microarray-based identification of htrA, a Streptoccocus pneumoniae gene that is regulated by the ciaRH two-component system and contributes to nasopharyngeal colonization. Infect. Immun. 2002, 70, 4059-4067.
134. Manganelli, R.; Voskuil, M. I.; Schoolnik, G. K.; Smith, I. The Mycobacterium tuberculosis ECF sigma factor sigma-(E): role in global gene expression and survival in macrophages. Mol. Microbiol. 2001, 41, 423-437.
135. Kaushal, D.; Schroeder, B. G.; Tyagi, S.; Yoshimatsu, T.; Scott, C.; Ko, C.; Carpenter, L.; Mehrota, J.; Manabe, Y. C.; Fleischmann, R. D.; Bishai, W. R. Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 8330-8335.
136. Hung, S. P.; Baldi, P.; Hatfield, G. W. Global gene expression profiling in Escherichia coli K12 - the effects of leucine-responsive regulatory protein. J. Biol. Chem. 2002, 277, 40309-40323.
137. Lehnen, D.; Blumer, C.; Polen, T.; Wackwitz, B.; Wendisch, V. F.; Unden, G. LrhA as a new transcriptional key regulator of flagella, motility, and chemotaxis genes in Escherichia coli. Mol. Microbiol. 2002, 45, 521-532.
138. Moreno, M. S.; Schneider, B. L.; Maile, R. R.; Weyler, W.; Saier, M. H. Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses. Mol. Microbiol. 2001, 39, 1366-1381.
139. Yoshida, K.; Kobayashi, K.; Miwa, Y.; Kang, C. M.; Matsunaga, M.; Yamaguchi, H.; Tojo, S.; Yamamoto, M.; Nishi, R.; Ogasawara, N.; Nakayama, T.; Fujita, Y. Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res. 2001, 29, 683-692.
140. Berka, R. M.; Hahn, J.; Albano, M.; Draskovic, I.; Persuh, M.; Cui, X. J.; Sloma, A.; Widner, W.; Dubnau, D. Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol. Microbiol. 2002, 43, 1331-1345.
141. Ogura, M.; Yamaguchi, H.; Kobayashi, K.; Ogasawara, N.; Fujita, Y.; Tanaka, T. Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J. Bacteriol. 2002, 184, 2344-2351.
142. Chaussee, M. S.; Sylva, G. L.; Studervant, D. E.; Smoot, L. M.; Graham, M. R.; Watson, R. O.; Musser, J. M. Rgg influences the expression of multiple regulatory loci to coregulate virulence factor expression in Streptoccocus pyogenes. Infect. Immun. 2002, 70, 762-770.
143. Clements, M. O.; Eriksson, S.; Thompson, A.; Lucchini, S.; Hinton, J. C. D.; Normark, S.; Rhen, M. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 8784-8789.
144. White, D. The Physiology and Biochemistry of Prokaryotes; Oxford University Press: New York, 2000.
145. Ninfa, A. J. Regulation of gene transcription by extracellular stimuli. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed.; Niedhardt et al., Eds.; American Society for Microbiology: Washington, DC, 1996; pp 1246-1262.
146. Oshima, T.; Aiba, H.; Masuda, Y.; Kanaya, S.; Sugiura, M.; Wanner, B. L.; Mori, H.; Mizuno, T. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol. Microbiol. 2002, 46, 281-291.
147. Kobayashi, K.; Ogura, M.; Yamaguchi, H.; Yoshida, K. I.; Ogasawara, N.; Tanaka, T.; Fujita, Y. Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. J. Bacteriol. 2001, 183, 7365-7370.
148. Zimmer, D. P.; Soupene, E.; Lee, H. L.; Wendisch, V. F.; Khodursky, A. B.; Peter, B. J.; Bender, R. A.; Kustu, S. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14674-14679.
149. Rodriguez, G. M.; Voskuil, M. I.; Gold, B.; Schoolnik, G. K.; Smith, I. ideR, an essential gene in Mycobacterium tuberculosis: role of ideR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002, 70, 3371-3381.
150. 2+-sensing sytem negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell 2002, 14, 2901-2913.
151. Graham, M. R.; Smoot, L. M.; Migliaccio, C. A. L.; Virtaneva, K.; Studervant, D. E.; Porcella, S. F.; Federle, M. J.; Adams, G. J.; Scott, J. R.; Musser, J. M. Virulence control in group A Streptoccocus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 13855-13860.
152. Stephens, C. Bacterial cell cycle: seeing the big picture with microarrays. Curr. Biol. 2001, 11, R222-R225.
153. Rohlin, L.; Oh, M. K.; Liao, J. C. DNA microarray for microbial technology: gene expression profiles in Escherichia coli during protein overexpression. J. Chin. Inst. Chem. Eng. 2002, 33, 103-112.
154. Jürgen, B.; Hanschke, R.; Sarvas, M.; Hecker, M.; Schweder, T. Proteome and transcriptome based analysis of Bacillus subtilis cells overproducing an insoluble heterologous protein. Appl. Microbiol. Biotechnol. 2001, 55, 326-332.
155. Oh, M.-K.; Liao, J. C. DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli. Metab. Eng. 2000, 2, 201-209.
156. Yoon, S. H.; Han, M.-J.; Lee, S. Y.; Jeong, K. J.; Yoo, J.-S. Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol. Bioeng. 2003, 81, 753-767.
157. Gill, R. T.; DeLisa, M. P.; Valdes, J. J.; Bentley, W. E. Genomic analysis of high-cell density recombinant Escherichia coli fermentation and "cell conditioning" for improved recombinant protein yield. Biotechnol. Bioeng. 2001, 72, 85-95.
158. Gonzalez, R.; Tao, H.; Purvis, J. E.; York, S. W.; Shanmugam, K. T.; Ingram, L. O. Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol. Prog. 2003, 19, 612-623.
159. Tomas, C A.; Keith, V. A.; Hendrik, P. J.; Bonarius, W. T.; Hendriksen, H. Y.; Beamish, J. A.; Paredes, C. J.; Eleftherios, T. P. DNA array-based transcriptional analysis of asporogenous, nonsolventogenic Clostridium acetobutylicum strains SKO1 and M5. J. Bacteriol. 2003, 185, 4539-4547.
160. Tummala, S. B.; Junne, S. G.; Paredes, C. J.; Papoutsakis, E. T. Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum strains. Biotechnol. Bioeng. 2003, 84, 842-854.
161. Hieter, P.; Boguski, M. Functional genomics: it's all how you read it. Science 1997, 278, 601-602.
162. Ideker, T.; Galitski, T.; Hood, L. A new approach to decoding life: Systems biology. Annu. Rev. Genomics Hum. Genet. 2001, 2, 343-372.
163. Henry, C. M. Systems biology: integrative approach to drug discovery. Chem. Eng. News 2003, 81, 45-55.