Plant functional genomics: Opportunities in microarray databases and data mining

Functional Plant Biology

Volumn 31, Issue 4, 2004, Pages 295-314

  Kennedy, Gavin C ^a   Wilson, Iain W ^a  

^a CSIRO   (Australia)

Author keywords

Data mining; Database; eQTL; Functional bioinformatics; Gene expression; Genomics; in silico analysis; Microarray; Molecular phenotype; Systems biology; Transcriptomics

Indexed keywords

DATA MINING; DATABASE SYSTEMS; FUNCTIONS; GENES;

FUNCTIONAL GENOMICS; GENE EXPRESSIONS;

PLANTS (BOTANY);

GENE EXPRESSION;

EMBRYOPHYTA;

EID: 2542611479     PISSN: 14454408     EISSN: None     Source Type: Journal    
DOI: 10.1071/FP03216     Document Type: Review

References (61)

1. Aharoni A, Keizer LC, Bouwmeester HJ, Sun Z, Alvarez-Huerta M, et al. (2000) Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. The Plant Cell 12, 647-662. doi:10.1105/TPC.12.5.647
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403-410. doi:10.1006/JMB1.1990.9999
3. Anderle P, Duval M, Draghici S, Kuklin A, Littlejohn TG, Medrano JF, Vilanova D, Roberts MA (2003) Gene expression databases and data mining. BioTechniques (Supplement), 36-44.
4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815. doi:10.1038/35048692
5. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, et al. (2002) Standards for microarray data. Science 298, 539. doi:10.1126/SCIENCE.298. 5593.539B
6. Baxevanis AD (2003) The molecular biology database collection: 2003 update. Nucleic Acids Research 31, 1-12. doi:10.1093/NAR/GKG120
7. Bouche N, Bouchez D (2001) Arabidopsis gene knockout: phenotypes wanted. Current Opinions in Plant Biology 4, 111-117. doi:10.1016/S1369-5266(00)00145-X
8. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29, 365-371. doi:10.1038/NG1201-365
9. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, et al. (2003) ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 31, 68-71. doi:10.1093/NAR/GKG091
10. Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, et al. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. The Plant Cell 14, 559-574. doi:10.1105/TPC.010410
11. D'Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16, 707-726. doi:10.1093/BIOINFORMATICS/16.8.707
12. Dudoit S, Yang YH, Speed TP, Callow MJ (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 12, 111-139.
13. Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research 30, 207-210. doi:10.1093/NAR/30.1.207
14. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences USA 95, 14863-14868. doi:10.1073/PNAS.95.25.14863
15. Fernie AR (2003) Metabolome characterisation in plant system analysis. Functional Plant Biology 30, 111-120. doi:10.1071/FP02163
16. Ge H, Walhout AJ, Vidal M (2003) Integrating 'omic' information: a bridge between genomics and systems biology. Trends in Genetics 19, 551-560. doi:10.1016/J.TIG.2003.08.009
17. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, et al. (2003) The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Research 31, 94-96. doi:10.1093/NAR/GKG078
18. Harmer SL, Kay SA (2000) Microarrays: determining the balance of cellular transcription. The Plant Cell 12, 613-616. doi:10.1105/TPC.12.5.613
19. Heazlewood JL, Millar AH (2003) Integrated plant proteomics - putting the green genomes to work. Functional Plant Biology 30, 471-482. doi:10.1071/FP03036
20. Helliwell CA, Chin-Atkins AN, Wilson IW, Chapple R, Dennis ES, Chaudhury A (2001) The Arabidopsis AMPI gene encodes a putative glutamate carboxypeptidase. The Plant Cell 13, 2115-2125. doi:10.1105/TPC.13.9.2115
21. Hilson P, Small I, Kuiper MT (2003) European consortia building integrated resources for Arabidopsis functional genomics. Current Opinions in Plant Biology 6, 426-429. doi:10.1016/S1369-5266(03)00086-4
22. Horvath DP, Schaffer R, West M, Wisman E (2003) Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species. The Plant Journal 34, 125-134.
23. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nature Biotechnology 19, 342-347. doi:10.1038/86730
24. Hulzink RJ, Weerdesteyn H, Croes AF, Gerats T, van Herpen MM, van Helden J (2003) In silico identification of putative regulatory sequence elements in the 5′-untranslated region of genes that are expressed during male gametogenesis. Plant Physiology 132, 75-83. doi:10.1104/PP.102.014894
25. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics 5, 299-314.
26. 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. The Plant Cell 13, 889-905. doi:10.1105/TPC.13.4.889
27. Kehoe DM, Villand P, Somerville S (1999) DNA microarrays for studies of higher plants and other photosynthetic organisms. Trends in Plant Science 4, 38-41. doi:10.1016/S1360-1385(98)01354-5
28. Kitano H (2002) Systems biology: a brief overview. Science 295, 1662-1664. doi:10.1126/SCIENCE.1069492
29. Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES (2002) Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. The Plant Cell 14, 2481-2494. doi:10.1105/TPC.004747
30. Kwon AT, Hoos HH, Ng R (2003) Inference of transcriptional regulation relationships from gene expression data. Bioinformatics 19, 905-912. doi:10.1093/BIOINFORMATICS/BTG106
31. Lahner B, Gong J, Mahmoudian M, Smith EL, Abid KB, et al. (2003) Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nature Biotechnology 21, 1215-1221. doi:10.1038/NBT865
32. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nature Genetics 21, 20-24. doi:10.1038/4447
33. Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405, 827-836. doi:10.1038/35015701
34. Maleck K, Levine A, Eulgem T, Morgan A, Schmid J, Lawton KA, Dangl JL, Dietrich RA (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genetics 26, 403-410. doi:10.1038/82521
35. Mangalam H, Stewart J, Zhou J, Schlauch K, Waugh M, Chen G, Farmer AD, Colello G, Weller JW (2001) GeneX: an open source gene expression database and integrated tool set. IBM Systems Journal 40, 552-569.
36. Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M (2003) Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends in Genetics 19, 570-577. doi:10.1016/J.TIG.2003.08.006
37. Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiology 132, 453-460. doi:10.1104/PP.102. 017236
38. Quackenbush J (2001) Computational analysis of microarray data. Nature Reviews. Genetics 2, 418-427. doi:10.1038/35076576
39. Quackenbush J (2002) Microarray data normalization and transformation. Nature Genetics 32 (Supplement), 496-501. doi:10.1038/NG1032
40. Reymond P, Weber H, Damond M, Farmer EE (2000) Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis. The Plant Cell 12, 707-720. doi:10.1105/TPC.12.5.707
41. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM (2002) Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Research 62, 4427-4433.
42. Richmond T, Somerville S (2000) Chasing the dream: plant EST microarrays. Current Opinions in Plant Biology 3, 108-116. doi:10.1016/SI369-5266(99)00049-7
43. Rombauts S, Dehais P, Van Montagu M, Rouze P (1999) PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Research 27, 295-296. doi:10.1093/NAR/27.1.295
44. Rossel JB, Wilson IW, Pogson BJ (2002) Global changes in gene expression in response to high light in Arabidopsis. Plant Physiology 130, 1109-1120. doi:10.1104/PP.005595
45. Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C (2002) BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biology 3 SOFTWARE0003.
46. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302. doi:10.1038/NATURE01434
47. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
48. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, et al. (2001) The Stanford microarray database. Nucleic Acids Research 29, 152-155. doi:10.1093/NAR/29.1.152
49. Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology 3, research0046.1-0046.9. doi:10.1186/GB-2002-3-9- RESEARCH0046
50. Stein L (2002) Creating a bioinformatics nation. Nature 417, 119-120. doi:10.1038/417119A
51. Stevens RD, Robinson AJ, Goble CA (2003) MyGrid: personalised bioinformatics on the information grid. Bioinformatics 19 (Supplement 1), i302-i304. doi:10.1093/BIOINFORMATICS/BTG1041
52. Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J, Shen-Orr S, Overton GC (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17, 300-308. doi:10.1093/BIOINFORMATICS/17.4.300
53. Thibaud-Nissen F, Shealy RT, Khanna A, Vodkin LO (2003) Clustering of microarray data reveals transcript patterns associated with somatic embryogenesis in soybean. Plant Physiology 132, 118-136. doi:10.1104/PP.103. 019968
54. Thijs G, Lescot M, Marchai K, Rombauts S, De Moor B, Rouze P, Moreau Y (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17, 1113-1122. doi:10.1093/BIOINFORMATICS/17.12.1113
55. Thijs G, Marchai K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y (2002) A Gibbs sampling method to detect over-represented motifs in the upstream regions of coexpressed genes. Journal of Computational Biology 9, 447-464. doi:10.1089/10665270252935566
56. Wasserman WW, Krivan W (2003) In silico identification of metazoan transcriptional regulatory regions. Die Naturwissenschaften 90, 156-166.
57. Wilkinson MD, Links M (2002) BioMOBY: an open-source biological web services proposal. Briefings in Bioinformatics 3, 331-341.
58. Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-1332. doi:10.1093/BIOINFORMATICS/BTG146
59. Wisman E, Ohlrogge J (2000) Arabidopsis microarray service facilities. Plant Physiology 124, 1468-1471. doi:10.1104/PP.124.4.1468
60. Wullschleger SD, Difazio SP (2003) Emerging use of gene expression microarrays in plant physiology. Comparative and Functional Genomics 4, 216-224. doi:10.1002/CFG.277
61. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30, e15. doi:10.1093/NAR/30.4.E15