Global analysis of gene expression using GeneChip microarrays

Current Opinion in Plant Biology

Volumn 6, Issue 5, 2003, Pages 418-425

  Zhu, Tong ^a  

^a SYNGENTA BIOTECHNOLOGY INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA; EUKARYOTA;

EID: 0141725448     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(03)00083-9     Document Type: Review

References (74)

1. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
2. Aharoni A, Vorst O: DNA microarrays for functional plant genomics. Plant Mol Biol 2002, 48:99-118.
3. Donson J, Fang Y, Espiritu-Santo G, Xing W, Salazar A, Miyamoto S, Armendarez V, Volkmuth W: Comprehensive gene expression analysis by transcript profiling. Plant Mol Biol 2002, 48:75-97.
4. Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, Verhoeven HA, Blaas J, van Houwelingen AM, De Vos RC, van der Voet H et al.: Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 2000, 12:647-662.
5. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert HJ: Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 2001, 13:889-905.
6. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K: OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J 2003, 33:751-763.
7. Negishi T, Nakanishi H, Yazaki J, Kishimoto N, Fujii F, Shimbo K, Yamamoto K, Sakata K, Sasaki T, Kikuchi S et al.: cDNA microarray analysis of gene expression during Fe-deficiency stress in barley suggests that polar transport of vesicles is implicated in phytosiderophore secretion in Fe-deficient barley roots. Plant J 2002, 30:83-94.
8. Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlandsson R, Blomqvist K, Bhalerao R, Uhlen M, Teeri TT, Lundeberg J et al: A transcriptional roadmap to wood formation. Proc Natl Acad Sci USA 2001, 98:14732-14737.
9. Whetten R, Sun YH, Zhang Y, Sederoff R: Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol Biol 2001, 47:275-291.
10. Heath LS, Ramakrishnan N, Sederoff RR, Whetten RW, Chevone BI, Struble CI, Jouenne VY, Chen D, van Zyl L, Grene R: Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system. Comp Funct Genomics 2002, 3:226-243.
11. Schaffer R, Landgraf J, Perez-Amador M, Wisman E: Monitoring genome-wide expression in plants. Curr Opin Biotechnol 2000, 11:162-167.
12. Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S: Microarray data quality analysis: lessons from the AFGC project. Plant Mol Biol 2002, 48:119-131.
13. Lipshultz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays. Nat Genet 1999, 21:20-24.
14. Zhu T, Wang X: Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol 2000, 124:1472-1476.
15. Zhu T, Chen W, Chang H-S, Provart N, Zou G, Glazebrook J, Wang X: Arabidopsis gene regulatory network revealed by whole genome expression analysis. Abstract 1-4, XIII International Conference on Arabidopsis Research, 2002, 28 June-2 July, Seville.
16. Town C, Haas B, Redman J, Tanimoto G: Development and evaluation of an Arabidopsis whole genome Affymetrix Chip. Abstract 1-21, XIII International Conference on Arabidopsis Research, 2002, 28 June-2 July, Seville.
17. Hunter BG, Beatty MK, Singletary GW, Hamaker BR, Dilkes BP, Larkins BA, Jung R: Maize opaque endosperm mutations create extensive changes in patterns of gene expression. Plant Cell 2002, 14:2591-2612.
18. Zhu T, Budworth P, Chen W, Provart N, Chang H-S, Guimil S, Su W, Estes B, Zou G, Wang X: Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotechnol J 2003, 1:59-70. A rice GeneChip microarray with modified design was developed to survey gene expression pattern during grain filling. Nutrient-partitioning genes from different pathways are coordinately expressed and may be regulated by the over-represented AACA element.
19. Wise R, Caldo R, Turner S, Ashlock D, Dickerson J: Parallel expression analysis using barley microarrays. Abstract W50, Plant & Animal Genomes XI Conference. 2003, 11-15 January, San Diego.
20. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittman M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675-1680.
21. Zhou Y, Abagyan R: Match-Only Integral Distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics 2002, 3:3.
22. Guigó R, Agarwal P, Abril JF, Burset M, Fickett JW: Gene prediction accuracy in large DNA sequences. Genome Res 2000, 10:1631-1642.
23. Zhu T, Chang H-S, Schmeits J, Gil P, Shi L, Budworth P, Zou G, Chen X, Wang X: Gene expression microarrays: improvements and applications towards agricultural gene discovery. J Assoc Lab Automat 2001, 6:95-98.
24. Zarrinkar PP, Mainquist JK, Zamora M, Stern D, Welsh JB, Sapinoso LM, Hampton GM, Lockhart DJ: Arrays of arrays for high-throughput gene expression profiling. Genome Res 2001, 11:1256-1261.
25. Zhu T, Budworth P, Han B, Brown D, Chang H-S, Zou Z, Wang X: Towards elucidating global gene expression in developing Arabidopsis: parallel analysis of 8300 genes. Plant Physiol Biocnem 2001, 39:221-242.
26. Cheong YH, Chang H-S, Gupta R, Wang X, Zhu T, Luan S: Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol 2002, 129:661-677.
27. Fowler S, Thomashow MF: Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 2002, 14:1675-1690.
28. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF: Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 2002, 130:2129-2141.
29. Menges M, Hennig L, Gruissem W, Murray JA: Cell cycle regulated gene expression in Arabidopsis. J Biol Chem 2002, 277:41987-42002. Multiple analysis approaches based on expression fluctuation pattern were used to identify 500 genes that are potentially regulated by the cell cycle.
30. Moseyko N, Zhu T, Chang H-S, Wang X, Feldman LJ: Transcription profiling of the early gravitropic response in Arabidopsis using high-density oligonucleotide probe microarrays. Plant Physiol 2002, 30:720-728.
31. Mussig C, Fischer S, Altmann T: Brassinosteroid-regulated gene expression. Plant Physiol 2002, 129:1241-1251.
32. Puthoff DP, Nettleton D, Rodermel SR, Baum TJ: Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. Plant J 2003, 33:911-921.
33. Whitham SA, Quan S, Chang HS, Cooper B, Estes B, Zhu T, Wang X, Hou YM: Diverse RNA viruses elicit the expression of common sets of genes in susceptible Arabidopsis thaliana plants. Plant J 2003, 33:271-283. Clustering the transcription profiles of Arabidopsis plants that had been infected with different RNA viruses revealed a common set of host genes for stress response and defense.
34. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA: Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000, 290:2110-2113.
35. Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou G, Whitham SA et al.: Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 2002, 14:559-574. The transcription signatures of diverse environmental stress conditions were used as indicators to classify the functions of 400 genes that encode stress-responsive transcription factors.
36. Ulm R, Ichimura K, Mizoguchi T, Peck SC, Zhu T, Wang X, Shinozaki K, Paszkowski J: Distinct regulation of salinity and genotoxic stress responses by Arabidopsis MAP kinase phosphatase 1. EMBO J 2002, 21:6483-6493.
37. Glazebrook J, Chen W, Estes B, Chang H-S, Nawrath C, Métraux J-P, Zhu T, Katagiri F: Topology of the network integrating salicylate and jasmonate signal transduction derived from global expression phenotyping. Plant J 2003, 34:217-228.
38. Moon Y-H, Chen L, Pan RL, Chang H-S, Zhu T, Maffeo DM, Sung ZR: EMF genes maintain vegetative development by repressing the flower program in Arabidopsis. Plant Cell 2003, 15:681-693.
39. Provart NJ, Gil P, Chen W, Han B, Chang H-S, Wang X, Zhu T: Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures. Plant Physiol 2003, 132:893-906.
40. Tao Y, Xie Z, Chen W, Glazebrook J, Chang H-S, Han B, Zhu T, Zou G, Katagiri F: Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell 2003, 15:317-330. The analysis of genome-wide transcription variations suggested that plant responses during an incompatible interaction are quantitatively different from those during a compatible interaction. This analysis led to a quantitative signaling model for compatible and incompatible pathogen interactions.
41. Vlachonasios KE, Thomashow MF, Triezenberg SJ: Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 2003, 15:626-638.
42. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G et al.: Experimental annotation of the human genome using microarray technology. Nature 2001, 409:922-927.
43. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR: Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002, 296:916-919. A GeneChip microarray with probes spaced on average every 35 base pairs along chromosomes 21 and 22 was used to detect transcribed sequences. The results showed that genomic sequence is transcribed and accounted for by the predicted and characterized exons.
44. Theologis A: Goodbye to 'one by one' genetics. Genome Biol 2001, 2:comment2004.1-2004.9 This review outlines the on-going efforts to map the transcriptional units of the Arabidopsis chromosome. More information can be obtained from the Salk Institute Genomic Analysis Laboratory (SIGNAL; http://signal. salk.edu).
45. Kim H, Snesrud EC, Haas B, Cheung F, Town CD, Quackenbush J: • Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res 2003, 13:327-340. The authors used amplicons of the 3′ ends of each predicted gene in Arabidopsis chromosome 2 as probes in a spotted chromosome microarray. Thus, they were able to verify the predicted genes experimentally according to their gene expression in various tissues and under a range of physiological conditions. This work provided clues as to the functions of many predicted genes.
46. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, •• Hannett NM, Harbison CT, Thompson CM, Simon I et al.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804. Network motifs were identified by the ChIP-Chip approach, and used to construct the transcription regulatory network.
47. Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA, Dangl JL, Dietrich RA: The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 2000, 26:403-410.
48. Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T, Somerville SC, Manners JM: Coordinated plant defense responses in Arabidopsis revealed by microarray analysis. Proc Natl Acad Sci USA 2000, 97:11655-11660.
49. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T et al.: Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 2002, 31:279-292.
50. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
51. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96:2907-2912.
52. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS: Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci USA 2000, 97:12182-12186.
53. Genoud T, Trevino Santa Cruz MB, Metraux JP: Numeric simulation of plant signaling networks. Plant Physiol 2001, 126:1430-1437.
54. Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, • Moreau Y: A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 2002, 9:447-464. The authors had previously modified the original Gibbs sampling algorithm and developed a popular program Motif Sampler for detecting overpresented sequence motifs. In this study, they validated the method by detecting three known cis-elements, including the G-box light-responsive element of plants, from microarray data.
55. Rombauts S, Dehais P, Van Montagu M, Rouze P: PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res 1999, 27:295-296.
56. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E et al.: Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
57. Zik M, Irish VF: Global identification of target genes regulated by • APETALA3 and PISTILLATA floral homeotic gene action. Plant Cell 2003, 15:207-222. Promoter fragments of target genes that are associated with the transcription factors APETALA3 (AP3) and PISTILLATA (PI) were enriched and isolated by Chromatin immuno-precipitation. These target genes were then identified by preferential hybridization to a microarray.
58. Tepperman JM, Zhu T, Chang H-S, Wang X, Quail PH: Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA 2001, 98:9437-9442.
59. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB: Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002, 109:307-320.
60. Stone JR, Wray GA: Rapid evolution of cis-regulatory sequences via local point mutations. Mol Biol Evol 2001, 18:1764-1770.
61. Streelman JT, Kocher TD: From phenotype to genotype. Evol Dev 2000, 2:166-173.
62. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW: Direct allelic variation scanning of the yeast genome. Science 1998, 281:1194-1197.
63. Borevitz JO, Liang D, Plouffe D, Chang H-S, Zhu T, Weigel D, • Berry CC, Winzeler E, Chory J: Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 2003, 13:513-523. The authors used a GeneChip microarray to detect gene-associated single-feature polymorphisms on a genome-wide scale by comparative genomic hybridization.
64. Chen W, Knoll D, Chang H-S, Han B, Zhu T: Transcription regulation of natural variation among Arabidopsis ecotypes, implications of evolutionary dynamics. Abstract 10-5, XIII International Conference on Arabidopsis Research, 2002, 28 June-2 July, Seville.
65. Wagner D: Chromatin regulation of plant development. Curr Opin Plant Biol 2003, 6:20-28.
66. Cohen BA, Mitra RD, Hughes JD, Church GM: A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26:183-186.
67. 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.: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291:1289-1292.
68. Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31:180-183.
69. Spellman PT, Rubin GM: Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 2002, 1:5.
70. Wayne ML, McIntyre LM: Combining mapping and arraying: an approach to candidate gene identification. Proc Natl Acad Sci USA 2002, 99:14903-14906.
71. Fiehn O, Kloska S, Altmann T: Integrated studies on plant biology using multiparallel techniques. Curr Opin Biotechnol 2001, 12:82-86.
72. Kamme F, Erlander MG: Global gene expression analysis of single cells. Curr Opin Drug Discov Devel 2003, 6:231-236.
73. Nakazono M, Qiu F, Borsuk LA, Schnable PS: 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 2003, 15:583-596. Laser-capture microdissection (LCM) was applied to isolate homogeneous maize epidermal cells and vascular tissues for global gene expression analysis. The authors demonstrated the feasibility of high-resolution global gene expression analyses in plants.
74. Hertzberg M, Sievertzon M, Aspeborg H, Nilsson P, Sandberg G, Lundeberg J: cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol. Plant J 2001, 25:585-591.