Using DNA microarrays to assay part function

Methods in Enzymology

Volumn 497, Issue , 2011, Pages 75-113

  Rhodius, Virgil A ^a,b   Gross, Carol A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; COMPLEMENTARY DNA;

ARTICLE; BACTERIAL GENE; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SYNTHESIS; GENE EXPRESSION; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; CARBOCYANINES; FLUORESCENT DYES; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RESEARCH DESIGN; RNA; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 79957456837     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385075-100004-4     Document Type: Article

References (73)

1. D.B. Allison, G.L. Gadbury, M.S. Heo, J.R. Fernandez, C.K. Lee, T.A. Prolla, and R. Weindruch A mixture model approach for the analysis of microarray gene expression data Comput. Stat. Data Anal. 39 2002 1 20
2. D.B. Allison, X. Cui, G.P. Page, and M. Sabripour Microarray data analysis: From disarray to consolidation and consensus Nat. Rev. Genet. 7 2006 55 65 (Pubitemid 41828948)
3. M. Arifuzzaman, M. Maeda, A. Itoh, K. Nishikata, C. Takita, R. Saito, T. Ara, K. Nakahigashi, H.C. Huang, A. Hirai, K. Tsuzuki, and S. Nakamura Large-scale identification of protein-protein interaction of Escherichia coli K-12 Genome Res. 16 2006 686 691
4. F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, and K. Struhl Current Protocols in Molecular Biology. 1998 John Wiley & Sons, Inc, Hoboken, NJ, USA
5. P. Baldi, and A.D. Long A Bayesian framework for the analysis of microarray expression data: Regularized t -test and statistical inferences of gene changes Bioinformatics 17 2001 509 519 (Pubitemid 32600497)
6. C.A. Ball, A. Brazma, H. Causton, S. Chervitz, R. Edgar, P. Hingamp, J.C. Matese, H. Parkinson, J. Quackenbush, M. Ringwald, S.A. Sansone, and G. Sherlock Submission of microarray data to public repositories PLoS Biol. 2 2004 E317
7. T. Bammler, R.P. Beyer, S. Bhattacharya, G.A. Boorman, A. Boyles, B.U. Bradford, R.E. Bumgarner, P.R. Bushel, K. Chaturvedi, D. Choi, M.L. Cunningham, and S. Deng Standardizing global gene expression analysis between laboratories and across platforms Nat. Methods 2 2005 351 356
8. C.L. Beisel, and G. Storz Base pairing small RNAs and their roles in global regulatory networks FEMS Microbiol. Rev. 34 2010 866 882
9. Y. Benjamini, and Y. Hochberg Controlling the false discovery rateA practical and powerful approach to multiple testing J. R. Stat. Soc. B Methodol. 57 1995 289 300
10. S. Beyhan, and F. Yildiz Bacterial gene expression analysis using microarrays J. Vis. Exp. 4 2007 206
11. B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 19 2003 185 193 (Pubitemid 36181903)
12. D. Botwell, and J. Sambrook DNA Microarrays: A Molecular Cloning Manual 2003 Cold Spring Harbor Press New York
13. P.C. Boutros, and A.B. Okey Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data Brief. Bioinform. 6 2005 331 343 (Pubitemid 43091939)
14. W.S. Branham, C.D. Melvin, T. Han, V.G. Desai, C.L. Moland, A.T. Scully, and J.C. Fuscoe Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements BMC Biotechnol. 7 2007 8
15. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, and P. Glenisson Minimum information about a microarray experiment (MIAME)-toward standards for microarray data Nat. Genet. 29 2001 365 371 (Pubitemid 34326681)
16. G. Butland, J.M. Peregrin-Alvarez, J. Li, W. Yang, X. Yang, V. Canadien, A. Starostine, D. Richards, B. Beattie, N. Krogan, M. Davey, and J. Parkinson Interaction network containing conserved and essential protein complexes in Escherichia coli Nature 433 2005 531 537 (Pubitemid 40204311)
17. B.K. Cho, K. Zengler, Y. Qiu, Y.S. Park, E.M. Knight, C.L. Barrett, Y. Gao, and B.O. Palsson The transcription unit architecture of the Escherichia coli genome Nat. Biotechnol. 27 2009 1043 1049
18. M.J. Czar, J.C. Anderson, J.S. Bader, and J. Peccoud Gene synthesis demystified Trends Biotechnol. 27 2009 63 72
19. S. Datta Empirical Bayes screening of many p-values with applications to microarray studies Bioinformatics 21 2005 1987 1994 (Pubitemid 40668036)
20. P. D'Haeseleer How does gene expression clustering work? Nat. Biotechnol. 23 2005 1499 1501 (Pubitemid 41752926)
21. K.A. Do, P. Muller, and F. Tang A Bayesian mixture model for differential gene expression J. R. Stat. Soc. C Appl. Stat. 54 2005 627 644 (Pubitemid 40653851)
22. S. Dudoit, J.P. Shaffer, and J.C. Boldrick Multiple hypothesis testing in microarray experiments Stat. Sci. 18 2003 71 103 (Pubitemid 41461823)
23. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl. Acad. Sci. USA 95 1998 14863 14868 (Pubitemid 29003722)
24. M.B. Elowitz, and S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 403 2000 335 338 (Pubitemid 30062393)
25. T.L. Fare, E.M. Coffey, H. Dai, Y.D. He, D.A. Kessler, K.A. Kilian, J.E. Koch, E. LeProust, M.J. Marton, M.R. Meyer, R.B. Stoughton, and G.Y. Tokiwa Effects of atmospheric ozone on microarray data quality Anal. Chem. 75 2003 4672 4675 (Pubitemid 37082262)
26. M.J. Filiatrault, P.V. Stodghill, P.A. Bronstein, S. Moll, M. Lindeberg, G. Grills, P. Schweitzer, W. Wang, G.P. Schroth, S. Luo, I. Khrebtukova, and Y. Yang Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity J. Bacteriol. 192 2010 2359 2372
27. H. Gao, Z.K. Yang, T.J. Gentry, L. Wu, C.W. Schadt, and J. Zhou Microarray-based analysis of microbial community RNAs by whole-community RNA amplification Appl. Environ. Microbiol. 73 2007 563 571 (Pubitemid 46147587)
28. D.G. Gibson, G.A. Benders, K.C. Axelrod, J. Zaveri, M.A. Algire, M. Moodie, M.G. Montague, J.C. Venter, H.O. Smith, and C.A. Hutchison 3rd One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome Proc. Natl. Acad. Sci. USA 105 2008 20404 20409
29. D.G. Gibson, L. Young, R.Y. Chuang, J.C. Venter, C.A. Hutchison 3rd, and H.O. Smith Enzymatic assembly of DNA molecules up to several hundred kilobases Nat. Methods 6 2009 343 345
30. M. Guell, V. van Noort, E. Yus, W.H. Chen, J. Leigh-Bell, K. Michalodimitrakis, T. Yamada, M. Arumugam, T. Doerks, S. Kuhner, M. Rode, and M. Suyama Transcriptome complexity in a genome-reduced bacterium Science 326 2009 1268 1271
31. T.S. Ham, S.K. Lee, J.D. Keasling, and A.P. Arkin Design and construction of a double inversion recombination switch for heritable sequential genetic memory PLoS ONE 3 2008 e2815
32. M.R. Hemm, B.J. Paul, T.D. Schneider, G. Storz, and K.E. Rudd Small membrane proteins found by comparative genomics and ribosome binding site models Mol. Microbiol. 70 2008 1487 1501
33. M.R. Hemm, B.J. Paul, J. Miranda-Rios, A. Zhang, N. Soltanzad, and G. Storz Small stress response proteins in Escherichia coli: Proteins missed by classical proteomic studies J. Bacteriol. 192 2010 46 58
34. J.P. Ioannidis, D.B. Allison, C.A. Ball, I. Coulibaly, X. Cui, A.C. Culhane, M. Falchi, C. Furlanello, L. Game, G. Jurman, J. Mangion, and T. Mehta Repeatability of published microarray gene expression analyses Nat. Genet. 41 2009 149 155
35. R.A. Irizarry, B.M. Bolstad, F. Collin, L.M. Cope, B. Hobbs, and T.P. Speed Summaries of Affymetrix GeneChip probe level data Nucleic Acids Res. 31 2003 e15
36. R.A. Irizarry, B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 2003 249 264
37. R.A. Irizarry, D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, E. Gabrielson, J.G. Garcia, J. Geoghegan, G. Germino, C. Griffin, and S.C. Hilmer Multiple-laboratory comparison of microarray platforms Nat. Methods 2 2005 345 350
38. J.E. Larkin, B.C. Frank, H. Gavras, R. Sultana, and J. Quackenbush Independence and reproducibility across microarray platforms Nat. Methods 2 2005 337 344
39. M.L. Lee, and G.A. Whitmore Power and sample size for DNA microarray studies Stat. Med. 21 2002 3543 3570 (Pubitemid 35363540)
40. S.K. Lee, H. Chou, T.S. Ham, T.S. Lee, and J.D. Keasling Metabolic engineering of microorganisms for biofuels production: From bugs to synthetic biology to fuels Curr. Opin. Biotechnol. 19 2008 556 563
41. S.S. Li, J. Bigler, J.W. Lampe, J.D. Potter, and Z. Feng FDR-controlling testing procedures and sample size determination for microarrays Stat. Med. 24 2005 2267 2280 (Pubitemid 41093914)
42. G. Nonaka, M. Blankschien, C. Herman, C.A. Gross, and V.A. Rhodius Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress Genes Dev. 20 2006 1776 1789 (Pubitemid 43992886)
43. B. Pieterse, R.H. Jellema, and M.J. van der Werf Quenching of microbial samples for increased reliability of microarray data J. Microbiol. Methods 64 2006 207 216 (Pubitemid 43112119)
44. S. Pounds, and S.W. Morris Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values Bioinformatics 19 2003 1236 1242 (Pubitemid 36850216)
45. J. Quackenbush Computational analysis of microarray data Nat. Rev. Genet. 2 2001 418 427 (Pubitemid 33673408)
46. M. Reich, T. Liefeld, J. Gould, J. Lerner, P. Tamayo, and J.P. Mesirov GenePattern 2.0 Nat. Genet. 38 2006 500 501
47. V.A. Rhodius, and J.T. Wade Technical considerations in using DNA microarrays to define regulons Methods 47 2009 63 72
48. V. Rhodius, T.K. Van Dyk, C. Gross, and R.A. LaRossa Impact of genomic technologies on studies of bacterial gene expression Annu. Rev. Microbiol. 56 2002 599 624 (Pubitemid 35217468)
49. V.A. Rhodius, W.C. Suh, G. Nonaka, J. West, and C.A. Gross Conserved and variable functions of the sigma(E) stress response in related genomes PLoS Biol. 4 2006 43 59
50. A.I. Saeed, N.K. Bhagabati, J.C. Braisted, W. Liang, V. Sharov, E.A. Howe, J. Li, M. Thiagarajan, J.A. White, and J. Quackenbush TM4 microarray software suite Methods Enzymol. 411 2006 134 193
51. D.W. Selinger, K.J. Cheung, R. Mei, E.M. Johansson, C.S. Richmond, F.R. Blattner, D.J. Lockhart, and G.M. Church RNA expression analysis using a 30 base pair resolution Escherichia coli genome array Nat. Biotechnol. 18 2000 1262 1268
52. C.M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, A. Sittka, S. Chabas, K. Reiche, J. Hackermuller, R. Reinhardt, P.F. Stadler, and J. Vogel The primary transcriptome of the major human pathogen Helicobacter pylori Nature 464 2010 250 255
53. L. Shi, L.H. Reid, W.D. Jones, R. Shippy, J.A. Warrington, S.C. Baker, P.J. Collins, F. de Longueville, E.S. Kawasaki, K.Y. Lee, Y. Luo, and Y.A. Sun The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat. Biotechnol. 24 2006 1151 1161 (Pubitemid 44359727)
54. L. Shi, R.G. Perkins, H. Fang, and W. Tong Reproducible and reliable microarray results through quality control: Good laboratory proficiency and appropriate data analysis practices are essential Curr. Opin. Biotechnol. 19 2008 10 18
55. G.K. Smyth Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat. Appl. Genet. Mol. Biol. 3 Article3 2004
56. R. Sorek, and P. Cossart Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity Nat. Rev. Genet. 11 2010 9 16
57. E.J. Steen, Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S.B. Del Cardayre, and J.D. Keasling Microbial production of fatty-acid-derived fuels and chemicals from plant biomass Nature 463 2010 559 562
58. J.D. Storey A direct approach to false discovery rates J. R. Stat. Soc. B Stat. Methodol. 64 2002 479 498
59. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, A. Paulovich, S.L. Pomeroy, T.R. Golub, E.S. Lander, and J.P. Mesirov Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. USA 102 2005 15545 15550 (Pubitemid 41528093)
60. J.J. Tabor, H.M. Salis, Z.B. Simpson, A.A. Chevalier, A. Levskaya, E.M. Marcotte, C.A. Voigt, and A.D. Ellington A synthetic genetic edge detection program Cell 137 2009 1272 1281
61. P. Tamayo, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation Proc. Natl. Acad. Sci. USA 96 1999 2907 2912 (Pubitemid 29148817)
62. S. Tavazoie, J.D. Hughes, M.J. Campbell, R.J. Cho, and G.M. Church Systematic determination of genetic network architecture Nat. Genet. 22 1999 281 285 (Pubitemid 29297256)
63. J. Taylor, R. Tibshirani, and B. Efron The "miss rate" for the analysis of gene expression data Biostatistics 6 2005 111 117 (Pubitemid 41240373)
64. M.K. Thomason, and G. Storz Bacterial antisense RNAs: How many are there, and what are they doing? Annu. Rev. Genet. 44 2010 167 188
65. J. Tian, K. Ma, and I. Saaem Advancing high-throughput gene synthesis technology Mol. Biosyst. 5 2009 714 722
66. R. Tibshirani A simple method for assessing sample sizes in microarray experiments BMC Bioinform. 7 2006 106
67. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. USA 98 2001 5116 5121 (Pubitemid 32397092)
68. C.A. Voigt Genetic parts to program bacteria Curr. Opin. Biotechnol. 17 2006 548 557 (Pubitemid 44442933)
69. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: A revolutionary tool for transcriptomics Nat. Rev. Genet. 10 2009 57 63
70. P.H. Westfall, and S.S. Young Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment 1993 Wiley New York
71. J.M. Wettenhall, and G.K. Smyth limmaGUI: A graphical user interface for linear modeling of microarray data Bioinformatics 20 2004 3705 3706 (Pubitemid 40136823)
72. Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30 2002 e15
73. K.Y. Yeung, D.R. Haynor, and W.L. Ruzzo Validating clustering for gene expression data Bioinformatics 17 2001 309 318 (Pubitemid 32421924)