Refinement of light-responsive transcript lists using rice oligonucleotide arrays: Evaluation of gene-redundancy

PLoS ONE

Volumn 3, Issue 10, 2008, Pages

  Jung, Ki Hong ^a   Dardick, Christopher ^b   Bartley, Laura E ^a   Cao, Peijian ^a   Phetsom, Jirapa ^a   Canlas, Patrick ^a   Seo, Young Su ^a   Shultz, Michael ^a   Ouyang, Shu ^c   Yuan, Qiaoping ^c,g   Frank, Bryan C ^c   Ly, Eugene ^c   Zheng, Li ^c   Jia, Yi ^d   Hsia, An Ping ^d   An, Kyungsook ^e   Chou, Hui Hsien ^d   Rocke, David ^a   Lee, Geun Cheol ^f   Schnable, Patrick S ^d   An, Gynheung ^e   Buell, C Robin ^c,h   Ronald, Pamela C ^a   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b APPALACHIAN FRUIT RESEARCH STATION   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d IOWA STATE UNIVERSITY   (United States)

^e Pohang University of Science and Technology (POSTECH)   (South Korea)

^f Konkuk University   (South Korea)

^g NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM   (United States)

^h MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC ORGANIZATION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOACTIVATION; PHOTORESPIRATION; PLANT GENETICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; TRANSCRIPTOMICS; CLUSTER ANALYSIS; ECONOMICS; EXPRESSED SEQUENCE TAG; GENETIC TRANSCRIPTION; GENETICS; LIGHT; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; PHYSIOLOGY; PLANT GENOME; RADIATION EXPOSURE; REPRODUCIBILITY;

ORYZA SATIVA;

VEGETABLE PROTEIN;

CLUSTER ANALYSIS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENOME, PLANT; LIGHT; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANT PROTEINS; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION, GENETIC;

EID: 53749099905     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003337     Document Type: Article

References (86)

1. Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, et al. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16: 1220-1234.
2. Tian C, Wan P, Sun S, Li J, Chen M (2004) Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol 54: 519-532.
3. Britten RJ (2005) The majority of human genes have regions repeated in other human genes. Proc Natl Acad Sci U S A 102: 5466-5470.
4. Sterck L, Rombauts S, Vandepoele K, Rouze P, Van de Peer Y (2007) How many genes are there in plants (... and why are they there)? Curr Opin Plant Biol 10: 199-203.
5. Green JA (2004) Defining the function of a prolactin gene family member. Proc Natl Acad Sci U S A 101: 16397-16398.
6. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
7. Ain R, Dai G, Dunmore JH, Godwin AR, Soares MJ (2004) A prolactin family paralog regulates reproductive adaptations to a physiological stressor. Proc Natl Acad Sci U S A 101: 16543-16548.
8. Stangeland B, Nestestog R, Grini PE, Skrbo N, Berg A, et al. (2005) Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5′ end of genes. J Exp Bot 56: 2495-2505.
9. Budhu A, Chen Y, Kim JW, Forgues M, Valerie K, et al. (2007) Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins. Carcinogenesis 28: 1552-1560.
10. Ding C, Peng H (2005) Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol 3: 185-205.
11. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, et al. (2000) Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1540.
12. Devos KM, Beales J, Nagamura Y, Sasaki T (1999) Arabidopsis-rice: will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res 9: 825-829.
13. Shimamoto K, Kyozuka J (2002) Rice as a model for comparative genomics of plants. Annu Rev Plant Biol 53: 399-419.
14. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot (Lond) 89: 3-10.
15. Jeon J, An G (2001) Gene tagging in rice: a high throughput system for functional genomics. Plant Sci 161: 211-219.
16. Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
17. Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12: 637-646.
18. Hiei Y, Komari T, Kubo T (1997) Transformation of rice mediated by Agrobacterium tumefaciens. Plant Mol Biol 35: 205-218.
19. IRGSP (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
20. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
21. Komari T, Hiei Y, Ishida Y, Kumashiro T, Kubo T (1998) Advances in cereal gene transfer. Curr Opin Plant Biol 1: 161-165.
22. Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
23. Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9: 91-101.
24. Jung KH, Han MJ, Lee YS, Kim YW, Hwang I, et al. (2005) Rice Undeveloped Tapetum1 is a major regulator of early tapetum development. Plant Cell 17: 2705-2722.
25. Ma L, Chen C, Liu X, Jiao Y, Su N, et al. (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15: 1274-1283.
26. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, et al. (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139: 822-835.
27. Shimono M, Sugano S, Nakayama A, Jiang CJ, Ono K, et al. (2007) Rice WRKY45 Plays a Crucial Role in Benzothiadiazole-Inducible Blast Resistance. Plant Cell 19: 2064-2076.
28. Jiao Y, Ma L, Strickland E, Deng XW (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256.
29. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143: 1467-1483.
30. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, et al. (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 138: 18-26.
31. Townsend JP, Cavalieri D, Hartl DL (2003) Population genetic variation in genome-wide gene expression. Mol Biol Evol 20: 955-963.
32. Rocke DM (2004) Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 15: 703-713.
33. Lu R, Lee GC, Shultz M, Dardick C, Jung K, et al. (2008) Assessing probe-specific dye and slide biases in two-color microarray data. BMC Bioinformatics 9: 314.
34. Rensink W, Hart A, Liu J, Ouyang S, Zismann V, et al. (2005) Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48: 598-605.
35. Ren XY, Fiers MW, Stiekema WJ, Nap JP (2005) Local coexpression domains of two to four genes in the genome of Arabidopsis. Plant Physiol 138: 923-934.
36. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, et al. (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 135: 745-755.
37. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
38. Werner T (2008) Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 19: 50-54.
39. Consortium. TGO (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36: D440-444.
40. Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, et al. (2005) Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics 5: 201-207.
41. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, et al. (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 63: 591-608.
42. Li M, Xu W, Yang W, Kong Z, Xue Y (2007) Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. Plant Physiol 144: 1797-1812.
43. Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258.
44. Johns MA, Mao L (2007) Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective. Funct Integr Genomics 7: 135-151.
45. Ip JY, Tong A, Pan Q, Topp JD, Blencowe BJ, et al. (2007) Global analysis of alternative splicing during T-cell activation. Rna 13: 563-572.
46. Goeman JJ, Buhlmann P (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23: 980-987.
47. Yang DH, Webster J, Adam Z, Lindahl M, Andersson B (1998) Induction of acclimative proteolysis of the light-harvesting chlorophyll a/b protein of photosystem II in response to elevated light intensities. Plant Physiol 118: 827-834.
48. Edwards JW, Coruzzi GM (1989) Photorespiration and light act in concert to regulate the expression of the nuclear gene for chloroplast glutamine synthetase. Plant Cell 1: 241-248.
49. Jung KH, Hur J, Ryu CH, Choi Y, Chung YY, et al. (2003) Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. Plant Cell Physiol 44: 463-472.
50. Stitt M, Kurzel B, Heldt HW (1984) Control of Photosynthetic Sucrose Synthesis by Fructose 2,6-Bisphosphate : II. Partitioning between Sucrose and Starch. Plant Physiol 75: 554-560.
51. Osterlund MT, Hardtke CS, Wei N, Deng XW (2000) Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405: 462-466.
52. Nyathi Y, Baker A (2006) Plant peroxisomes as a source of signalling molecules. Biochim Biophys Acta 1763: 1478-1495.
53. Corpas FJ, Barroso JB, del Rio LA (2001) Peroxisomes as a source of reactive oxygen species and nitric oxide signal molecules in plant cells. Trends Plant Sci 6: 145-150.
54. Yi C, Deng XW (2005) COP1-from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol 15: 618-625.
55. Richards KD, Schott EJ, Sharma YK, Davis KR, Gardner RC (1998) Aluminum induces oxidative stress genes in Arabidopsis thaliana. Plant Physiol 116: 409-418.
56. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, et al. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130: 2129-2141.
57. Abdel-Ghany SE, Muller-Moule P, Niyogi KK, Pilon M, Shikanai T (2005) Two P-type ATPases are required for copper delivery in Arabidopsis thaliana chloroplasts. Plant Cell 17: 1233-1251.
58. Jung KH, Han MJ, Lee DY, Lee YS, Schreiber L, et al. (2006) Wax-deficient anther1 is involved in cuticle and wax production in rice anther walls and is required for pollen development. Plant Cell 18: 3015-3032.
59. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161.
60. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
61. Matsumoto F, Obayashi T, Sasaki-Sekimoto Y, Ohta H, Takamiya K, et al. (2004) Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system. Plant Physiol 135: 2379-2391.
62. Boldt R, Edner C, Kolukisaoglu U, Hagemann M, Weckwerth W, et al. (2005) D-GLYCERATE 3-KINASE, the last unknown enzyme in the photorespiratory cycle in Arabidopsis, belongs to a novel kinase family. Plant Cell 17: 2413-2420.
63. Somerville CR (2001) An early Arabidopsis demonstration. Resolving a few issues concerning photorespiration. Plant Physiol 125: 20-24.
64. Leegood RC (2007) A welcome diversion from photorespiration. Nat Biotechnol 25: 539-540.
65. Lan Y, Woodrow IE, Mott KA (1992) Light-Dependent Changes in Ribulose Bisphosphate Carboxylase Activase Activity in Leaves. Plant Physiol 99: 304-309.
66. Jung KH, Lee J, Dardick C, Seo YS, Cao P, et al. (2008) Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice. PLoS Genetics 4: e1000164.
67. Miki D, Itoh R, Shimamoto K (2005) RNA silencing of single and multiple members in a gene family of rice. Plant Physiol 138: 1903-1913.
68. Liepman AH, Olsen LJ (2001) Peroxisomal alanine : glyoxylate aminotransferase (AGT1) is a photorespiratory enzyme with multiple substrates in Arabidopsis thaliana. Plant J 25: 487-498.
69. Igarashi D, Miwa T, Seki M, Kobayashi M, Kato T, et al. (2003) Identification of photorespiratory glutamate:glyoxylate aminotransferase (GGAT) gene in Arabidopsis. Plant J 33: 975-987.
70. Kurek I, Chang TK, Bertain SM, Madrigal A, Liu L, et al. (2007) Enhanced Thermostability of Arabidopsis Rubisco activase improves photosynthesis and growth rates under moderate heat stress. Plant Cell 19: 3230-3241.
71. Sharma A, Komatsu S (2002) Involvement of a Ca(2+)-dependent protein kinase component downstream to the gibberellin-binding phosphoprotein, RuBisCO activase, in rice. Biochem Biophys Res Commun 290: 690-695.
72. Komatsu S, Konishi H, Shen S, Yang G (2003) Rice proteomics: a step toward functional analysis of the rice genome. Mol Cell Proteomics 2: 2-10.
73. Voll LM, Jamai A, Renne P, Voll H, McClung CR, et al. (2006) The photorespiratory Arabidopsis shm1 mutant is deficient in SHM1. Plant Physiol 140: 59-66.
74. Rohila JS, Chen M, Chen S, Chen J, Cerny R, et al. (2006) Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J 46: 1-13.
75. Wang YS, Pi LY, Chen X, Chakrabarty PK, Jiang J, et al. (2006) Rice XA21 binding protein 3 is a ubiquitin ligase required for full Xa21-mediated disease resistance. Plant Cell 18: 3635-3646.
76. Chou HH, Hsia AP, Mooney DL, Schnable PS (2004) Picky: oligo microarray design for large genomes. Bioinformatics 20: 2893-2902.
77. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-887.
78. Raghavachari N, Bao YP, Li G, Xie X, Muller UR (2003) Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride. Anal Biochem 312: 101-105.
79. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal Chem 75: 4672-4675.
80. Berger JA, Hautaniemi S, Jarvinen AK, Edgren H, Mitra SK, et al. (2004) Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5: 194.
81. Affymetrix (2001) Affymetrix Microarray Suite User Guide. Affymetrix.
82. Affymetrix (2002) Statistical algorithms description document. Affymetrix.
83. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666.
84. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
85. Pollock SV, Colombo SL, Prout DL Jr, Godfrey AC, Moroney JV (2003) Rubisco activase is required for optimal photosynthesis in the green alga Chlamydomonas reinhardtii in a low-CO(2) atmosphere. Plant Physiol 133: 1854-1861.
86. Reumann S, Weber AP (2006) Plant peroxisomes respire in the light: some gaps of the photorespiratory C2 cycle have become filled-others remain. Biochim Biophys Acta 1763: 1496-1510.