Methods for transcriptional profiling in plants. Be fruitful and replicate

Plant Physiology

Volumn 135, Issue 2, 2004, Pages 637-652

  Meyers, Blake C ^a   Galbraith, David W ^c   Nelson, Timothy ^b   Agrawal, Vikas ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 3042602438     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.040840     Document Type: Review

References (139)

1. Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O, et al (1995) Initial assessment of human gene diversity and expression patterns based on 83 million nucleotides of cDNA sequence. Nature 377: 3-174
2. Alonso-Blanco C, Koornneef M (2000) Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci 5: 22-29
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Asano T, Masumura T, Kusano H, Kikuchi S, Kurita A, Shimada H, Kadowaki K (2002) Construction of a specialized cDNA library from plant cells isolated by laser capture microdissection: toward comprehensive analysis of the genes expressed in the rice phloem. Plant J 32: 401-408
5. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995
6. Auer H, Lyianarachchi S, Newsom D, Klisovic MI, Marcucci U, Kornacker K (2003) Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet 35: 292-293
7. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741
8. Banks RE, Dunn MJ, Forbes MA, Stanley A, Pappin D, Naven T, Cough M, Harnden P, Selby PJ (1999) The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis-preliminary findings. Electrophoresis 20: 689-700
9. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ (2003) Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13: 1775-1785
10. Baum M, Bielau S, Rittner N, Schmid K, Eggelbusch K, Dahms M, Schlauersbach A, Tahedl H, Beier M, Guimil R, et al (2003) Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res 31: e151
11. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960
12. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101
13. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513-523
14. Brandt S, Kloska S, Altmann T, Kehr J (2002) Using array hybridization to monitor gene expression at the single cell level. J Exp Bot 53: 2315-2323
15. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29: 365-371
16. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, et al (2000a) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18: 630-634
17. Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C, Mao Jl, Luo S, Kirchner JJ, Eletr S, et al (2000b) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97: 1665-1670
18. Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29: 23-39
19. Cao YC, Jin R, Mirkin CA (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297: 1536-1540
20. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, et al (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291: 1289-1292
21. Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338
22. Chakravarthy S, Tuori RP, D'Ascenzo MD, Fobert PR, Despres C, Martin GB (2003) The tomato transcription factor Pti4 regulates defense-related gene expression via GCC box and non-GCC box cis elements. Plant Cell 15: 3033-3050
23. Cheung VG, Spielman RS (2002) The genetics of variation in gene expression. Nat Genet 32 (suppl.): 522-525
24. Christensen TM, Vejlupkova Z, Sharma YK, Arthur KM, Spatafora JW, Albright CA, Meeley RB, Duvick JP, Quatrano RS, Fowler JE (2003) Conserved subgroups and developmental regulation in the monocot rop gene family. Plant Physiol 133: 1791-1808
25. Chu TM, Weir B, Wolfinger R (2002) A systematic statistical linear modeling approach to oligonucleotide array experiments. Math Biosci 176: 35-51
26. Close TJ, Wanamaker S, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134: 960-968
27. Craven RA, Totty N, Harnden P, Selby PJ, Banks RE (2002) Laser capture microdissection and two-dimensional polyacrylamide gel electrophoresis: evaluation of tissue preparation and sample limitations. Am J Pathol 160: 815-822
28. Delseny M, Cooke R, Raynal M, Grellet F (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett 405: 129-132
29. Draghici S (2002) Statistical intelligence: effective analysis of high-density microarray data. Drug Discov Today 7: S55-S63
30. Draghici S, Kulaeva O, Hoff B, Petrov A, Shams S, Tainsky MA (2003) Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays. Bioinformatics 19: 1348-1359
31. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21: 10-14
32. Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2: 919-929
33. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186
34. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA (1996) Laser capture microdis-section. Science 274: 998-1001
35. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, et al (2002) Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343
36. Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9: 950-959
37. Fizames C, Munos S, Cazettes C, Nacry P, Boucherez J, Gaymard F, Piquemal D, Delorme V, Commes T, Doumas P, et al (2004) The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol 134: 67-80
38. Galbraith DW (2003) Global analysis of cell type-specific gene expression. Comp Funct Genomics 4: 208-215
39. Gibbings JG, Cook BP, Dufault MR, Madden SL, Khuri S, Turnbull CJ, Dun well JM (2003) Global transcript analysis of rice leaf and seed using SAGE technology. Plant Biotechnol J 1: 271-285
40. Ginzinger DG (2002) Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 30: 503-512
41. Goel A, Seth P, Chauhan SS (2001) Specific amplication of mRNA splice variants by RT-PCR. Biotechniques 30: 944-949
42. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
43. Gowda M, Jantasuriyarat C, Dean R, Wang G-L (2004) Robust-LongSAGE (RL-SAGE) for both gene discovery and transcriptome analysis. Plant Physiol 134: 890-897
44. Grant D, Cregan P, Shoemaker RC (2000) Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci USA 97: 4168-4173
45. Green CD, Simons JF, Taillon BE, Lewin DA (2001) Open systems: panoramic views of gene expression. J Immunol Methods 250: 67-79
46. Greller LD, Tobin FL (1999) Detecting selective expression of genes and proteins. Genome Res 9: 282-296
47. Guo M, Rupe MA, Danilevskaya ON, Yang X, Hu Z (2003) Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J 36: 30-44
48. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666
49. Hagiwara Y, Hirai M, Nishiyama K, Kanazawa I, Ueda T, Sakaki Y, Ito T (1997) Screening for imprinted genes by allelic message display: identification of a paternally expressed gene impact on mouse chromosome 18. Proc Natl Acad Sci USA 94: 9249-9254
50. Hayward-Lester A, Oefner PJ, Sabatini S, Doris PA (1995) Accurate and absolute quantitative measurement of gene expression by single-tube RT-PCR and HPLC. Genome Res 5: 494-499
51. Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6: 986-994
52. Hoth S, Ikeda Y, Morgante M, Wang X, Zuo J, Hanafey MK, Gaasterland T, Tingey SV, Chua NH (2003) Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Lett 554: 373-380
53. Hoth S, Morgante M, Sanchez JP, Hanafey MK, Tingey SV, Chua NH (2002) Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abil-1 mutant. J Cell Sci 115: 4891-4900
54. Hsieh WP, Chu TM, Wolfinger RD, Gibson G (2003) Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165: 747-757
55. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, et al (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347
56. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126
57. Ishii M, Hashimoto S, Tsutsumi S, Wada Y, Matsushima K, Kodama T, Aburatani H (2000) Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics 68: 136-143
58. Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17: 388-391
59. Jin L, Thompson CA, Qian X, Kuecker SJ, Kulig E, Lloyd RV (1999) Analysis of anterior pituitary hormone mRNA expression in immunophenotypically characterized single cells after laser capture microdissection. Lab Invest 79: 511-512
60. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29: 389-395
61. Jung SH, Lee JY, Lee DH (2003) Use of SAGE technology to reveal changes in gene expression in Arabidopsis leaves undergoing cold stress. Plant Mol Biol 52: 553-567
62. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919
63. Karrer EE, Lincoln JE, Hogenhout S, Bennett AB, Bostock RM, Martineau B, Lucas WJ, Gilchrist DG, Alexander D (1995) In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc Natl Acad Sci USA 92: 3814-3818
64. Kawamoto S, Yoshii J, Mizuno K, Ito K, Miyamoto Y, Ohnishi T, Matoba R, Hori N, Matsumoto Y, Okumura T, et al (2000) BodyMap: a collection of 3′ ESTs for analysis of human gene expression information. Genome Res 10: 1817-1827
65. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13: 889-905
66. Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132: 27-35
67. Kerr MK, Martin M, Churchill GA (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7: 819-837
68. Klein CA, Seidl S, Petat-Dutter K, Offner S, Geigl JB, Schmidt-Kittler O, Wendler N, Passlick B, Huber RM, Schlimok G, Baeuerle PA, Riethmuller G (2002) Combined transcriptome and genome analysis of single micrometastatic cells. Nat Biotechnol 20: 387-392
69. Klein D (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8: 257-260
70. Kuo WP, Jenssen T-K, Butte AJ, Ohno-Machado L, Kohane IS (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405-412
71. Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF (2000) SAGEmap: a public gene expression resource. Genome Res 10: 1051-1060
72. Lee H-S, Wang J, Tian L, Jiang H, Black MA, Madlung A, Watson B, Lukens L, Pires JC, Wang JJ, et al (2004) Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnol J 2: 45-57
73. Lee JY, Lee DH (2003) Use of serial analysis of gene expression technology to reveal changes in gene expression in Arabidopsis pollen undergoing cold stress. Plant Physiol 132: 517-529
74. Lee ML, Kuo FC, Whitmore GA, Sklar J (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 97: 9834-9839
75. Levsky JM, Shenoy SM, Pezo RC, Singer RH (2002) Single-cell gene expression profiling. Science 297: 836-840
76. Levsky JM, Singer RH (2003) Gene expression and the myth of the average cell. Trends Cell Biol 13: 4-6
77. Li C, Wong WH (2001a) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98: 31-36
78. Li C, Wong WH (2001b) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2: RESEARCH0032
79. Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, Lee MP (2003) Allelic variation in gene expression is common in the human genome. Genome Res 13: 1855-1862
80. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, et al (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680
81. Luo L, Salunga RC, Guo H, Bittner A, Joy KC, Galindo JE, Xiao H, Rogers KE, Wan JS, Jackson MR, et al (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med 5: 117-122
82. MacIntosh GC, Wilkerson C, Green PJ (2001) Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol 127: 765-776
83. Matsubara K, Okubo K (1993) cDNA analyses in the human genome project. Gene 135: 265-274
84. Matsumura H, Nirasawa S, Terauchi R (1999) Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J 20: 719-726
85. Matsumura H, Reich S, Ho A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci USA 100: 15718-15723
86. Mazur B, Krebbers E, Tingey S (1999) Gene discovery and product development for grain quality traits. Science 285: 372-375
87. Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM, Lu G, Fang J, Liu WM, Ryder T, et al (2003) Probe selection for high-density oligonucleotide arrays. Proc Natl Acad Sci USA 100: 11237-11242
88. Meyers BC, Lee DK, Vu TH, Tej SS, Edberg SB, Matvienko M, Tindell LD (2004a) Arabidopsis MPSS: an online resource for quantitative expression analysis. Plant Physiol 135: 801-813
89. Meyers BC, Tej SS, Vu TH, Haudenschild C, Agrawal V, Edberg SB, Ghazal H, Decola S (2004b) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res (in press)
90. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild C (2004c) Analysis of the transcriptional complexity of Arabidopsis by massively parallel signature sequencing. Nat Biotechnol (in press)
91. Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS (2004) Digital quantitative measurements of gene expression. Biotechnol Bioeng 86: 117-124
92. Mitra RD, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27: e34
93. Mitra RD, Shendure J, Olejnik J, Edyta Krzymanska O, Church GM (2003) Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 320: 55-65
94. Naef F, Hacker CR, Patil N, Magnasco M (2002) Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol 3: RESEARCH0018
95. Nakazono M, Qiu F, Borsuk LA, Schnable PS (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15: 583-596
96. Nam JM, Thaxton CS, Mirkin CA (2003) Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 301: 1884-1886
97. Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M, et al (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 106: 1241-1255
98. Nielsen HB, Wernersson R, Knudsen S (2003) Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res 31: 3491-3496
99. Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res 13: 1301-1306
100. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, et al (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12: 1749-1755
101. Oakey RJ, Beechey CV (2002) Imprinted genes: identification by chromosome rearrangements and post-genomic strategies. Trends Genet 18: 359-366
102. Ohyama H, Mahadevappa M, Luukkaa H, Todd R, Warrington JA, Wong DT (2002) Use of laser capture microdissection-generated targets for hybridization of high-density oligonucleotide arrays. Methods Enzymol 356: 323-333
103. Okubo K, Hori N, Matoba R, Niiyama T, Fukushima A, Kojima Y, Matsubara K (1992) Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat Genet 2: 173-179
104. Okubo K, Itoh K, Fukushima A, Yoshii J, Matsubara K (1995) Monitoring cell physiology by expression profiles and discovering cell type-specific genes by compiled expression profiles. Genomics 30: 178-186
105. Oleksiak MF, Churchill GA, Crawford DL (2002) Variation in gene expression within and among natural populations. Nat Genet 32: 261-266
106. Orphanides G, Reinberg D (2002) A unified theory of gene expression. Cell 108: 439-451
107. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, Lee HS, Comai L, Madlung A, Doerge RW, Colot V, et al (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19: 141-147
108. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263
109. Renner W, Pilger E (1999) Simultaneous in vivo quantitation of vascular endothelial growth factor mRNA splice variants. J Vasc Res 36: 133-138
110. Roberts JP (2002) The cutting edge in laser microdissection. Biophotonics International 9: 50-53
111. Russo G, Zegar C, Giordano A (2003) Advantages and limitations of microarray technology in human cancer. Oncogene 22: 6497-6507
112. Sana S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE (2002) Using the transcriptome to annotate the genome. Nat Biotechnol 20: 508-512
113. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
114. Shimkets RA, Lowe DG, Tai JT, Sehl P, Jin H, Yang R, Predki PF, Rothberg BE, Murtha MT, Roth ME, et al (1999) Gene expression analysis by transcript profiling coupled to a gene database query. Nat Biotechnol 17: 798-803
115. Simillion C, Vandepoele K, Van Montagu MC, Zabeau M, Van De Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sxi USA 99: 13627-13632
116. Simone NL, Paweletz CP, Charboneau L, Petricoin EF III, Liotta LA (2000) Laser capture microdissection: beyond functional genomics to proteomics. Mol Diagn 5: 301-307
117. Slonim DK (2002) From patterns to pathways: gene expression data analysis comes of age. Nat Genet 32 (suppl.): 502-508
118. Stekel DJ, Git Y, Falciani F (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10: 2055-2061
119. Stern MD, Anisimov SV, Boheler KR (2003) Can transcriptome size be estimated from SAGE catalogs? Bioinformatics 19: 443-448
120. Stollberg J, Urschitz J, Urban Z, Boyd CD (2000) A quantitative evaluation of SAGE. Genome Res 10: 1241-1248
121. Talla E, Tekaia F, Brino L, Dujon B (2003) A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics 4: 38
122. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 5676-5684
123. Vanhee-Brossollet C, Vaquero C (1998) Do natural antisense transcripts make sense in eukaryotes? Gene 211: 1-9
124. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484-487
125. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Mieter P, Vogelstein B, Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 88: 243-251
126. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117
127. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, et al (1998) Direct allelic variation scanning of the yeast genome. Science 281: 1194-1197
128. Wisman E, Ohlrogge J (2000) Arabidopsis microarray service facilities. Plant Physiol 124: 1468-1471
129. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637
130. Wong MH, Saam JR, Stappenbeck TS, Rexer CH, Gordon JI (2000) Genetic mosaic analysis based on Cre recombinase and navigated laser capture microdissection. Proc Natl Acad Sci USA 97: 12601-12606
131. Wortman JR, Haas BJ, Hannick Ll, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, et al (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468
132. Xiao YL, Malik M, Whitelaw CA, Town CD (2002) Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis. Plant Physiol 130: 2118-2128
133. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846
134. Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al (2003) Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379-386
135. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al (2002) A draft sequence of the rice genome (Onjza sativa L. ssp. indica). Science 296: 79-92
136. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30: e48
137. Zhang L, Zhou W, Velculescu VE, Kern SE, Hruban RH, Hamilton SR, Vogelstein B, Kinzler KW (1997) Gene expression profiles in normal and cancer cells. Science 276: 1268-1272
138. Zhu J, Shendure J, Mitra RD, Church GM (2003) Single molecule profiling of alternative pre-mRNA splicing. Science 301: 836-838
139. Zhu T, Wang X (2000) Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol 124: 1472-1476