Re-annotation of the maize oligonucleotide array

Maydica

Volumn 57, Issue 1, 2012, Pages 49-55

  Seifert, Felix ^a,b   Thiemann, Alexander ^a   Pospisil, Heike ^b   Scholten, Stefan ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

^b TECHNICAL UNIVERSITY OF APPLIED SCIENCES WILDAU   (Germany)

Author keywords

Annotation; Maize oligonucleotide array; Microarray

Indexed keywords

ZEA MAYS;

EID: 84872862732     PISSN: 00256153     EISSN: 22798013     Source Type: Journal    
DOI: None     Document Type: Article

References (46)

1. Alexa A, Rahnenfuhrer J, Lengauer T, 2006. Improved scoring of functional groups from gene expres sion data by decorrelating GO graph structure. Bioinformatics 22(13): 1600-1607
2. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A, 2009. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-D890
3. Barros E, Lezar S, Anttonen MJ, van Dijk JP, Rohlig RM, Kok EJ, Engel KH, 2010. Comparison of two GM maize varieties with a near-isogenic non-GM variety using transcriptomics, proteomics and metabolomics. Plant Biotechnology Journal 8(4): 436-451
4. Bosch M, Mayer CD, Cookson A, Donnison IS, 2011. Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes. J Exp Biol 62(10): 3545-3561
5. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL, 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421
6. Carbon S, Ireland A, Mungall C.J, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group, 2008. AmiGO: online access to ontology and annotation data. Bioinformatics 25(2): 288-289
7. Conesa A, Gotz S, 2008. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. Int J Plant Genomics 2008: 1-13
8. Covshoff S, Majeran W, Liu P, Kolkman JM, van Wijk KJ, Brutnell TP, 2008. Deregulation of maize C4 photosynthetic development in a mesophyll celldefective mutant. Plant Physiol 146(4): 1469-81
9. Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group, Lewis S, 2007. OBOEdit an ontology editor for biologists. Bioinformatics23 (16): 2198-2200
10. Fernandes J, Morrow DJ, Casati P, Walbot V, 2008. Distinctive transcriptome responses to adverse environmental conditions in Zea mays L. Plant Biotechnol J 6(8): 782-98
11. Gardiner JM, Buell CR, Elumalai R, Galbraith DW, Henderson DA, Iniguez AL, Kaeppler SM, Kim JJ, Liu J, Smith A, Zheng L, Chandler VL, 2005. Design, Production, and Utilization of Long Oligonucleotide Microarrays for Expression Analysis in Maize. Maydica 50: 425-435
12. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, lacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J, 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5 (10): R80
13. Hansen S, Horvath D, Jarachi Y, Carlson G, Clay D, 2011. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33494
14. Hayes KR, Beatty M, Meng X, Simmons CR, Habben JE, Danilevskaya ON, 2010. Maize Global Transcriptomics reveals Pervasive Leaf Diurnal Rhythms but Rhythms in Developing Ears are Largely Limited to the Core Oscillator. PloS ONE 5(9): e12887
15. Hayano-Kanashiro C, Calderón-Vázquez C, Ibarra Laclette E, Herrera-Estrella L, Simpson J, 2009. Analysis of gene expression and physiological responses in three Mexican maize landraces under drought stress and recovery irrigation. PloS One 4(10): e7531
16. Holding DR, Hunter BG, Chung T, Gibbon BC, Ford CF, Bharti AK, Messing J, Hamaker BR, Larkins BA, 2008. Genetic Analysis of opaque2 Modifier Loci in Quality Protein Maize. Theor Appl Genet 117(2): 157-170
17. Ito H, 2012. Small RNAs and transposon silencing in plants. Dev Growth Differ 54: 100-107
18. Jin H, Vacic V, Girke T, Lonardi S, Zhu JK, 2008. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Molecular Biol 9: 6
19. Johnson ET, Dowd PF, Liu ZL, Musser RO, 2011. Comparative transcription profiling analyses of maize reveals candidate defensive genes for seedling resistance against corn earworm. Mol Genet Genomics 285(6), 517-525
20. Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, Buckler ES, 2006. Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol 4, 489-498
21. Liu X, Fu J, Gu D, Liu W, Liu T, Peng Y, Wang J, Wang G, 2008. Genome-wide analysis of gene expression profiles during the kernel development of maize (Zea mays L.). Genomics 91(4): 378-87
22. Liu J, Han L, Chen F, Bao J, Zhang F, Mi G, 2008. Microarray analysis reveals early responsive genes possibly involved in localized nitrate stimulation of lateral root development in maize (Zea mays L.). Plant Sci 175(3): 272-282
23. Luo M, Brown RL, Chen ZY, Menkir A, Yu J, Bhatnagar D, 2011. Transcriptional Profiles Uncover Aspergillus flavus-Induced Resistance in Maize Kernels. Toxins 3(7): 766-786
24. Ma J, Morrow DJ, Fernandes J, Walbot V, 2006. Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biol 7: R22
25. Ma J, Skibbe DS, Fernandes J, Walbot V, 2008. Male reproductive development: gene expression profiling of maize anther and pollen ontogeny. Genome Biol 9: R181
26. Maron LG, Kirst M, Mao C, Milner MJ, Menossi M, Kochian LV, 2008. Transcriptional profiling of aluminum toxicity and tolerance responses in maize roots. New Phytol 179(1): 116-128
27. Moose S, Boddu J, 2010a. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17932
28. Moose S, Boddu J, 2010b. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17953
29. Moose S, Church J, 2009. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18011
30. Moose S, Zhao H, 2009. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18006
31. Moose S, Zhao H, 2010. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18008
32. Moriles J, Hansen S, Horvath D, Reicks G, Clay D, Clay S, 2012. Microarray and Growth Analyses Identify Differences and Similarities of Early Corn Response to Weeds, Shade, and Nitrogen Stress. Weed Sci 60(2): 158-166
33. Morrison KM, Simmons SJ, Stapleton AE, 2010. Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present. Physiol plantarum 140(4): 334-341
34. Phimister D, 1999. Going global. Nat Genet 21: 1
35. Riddle NC, Jiang H, An L, Doerge RW, Birchler JA, 2010. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theor Appl Genet 120(2): 341-353
36. Sawers RJH, Liu P, Anufrikova K, Hwang JTG, Brutnell TP, 2007. A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8: 12
37. Schena M, Shalon D, Davis RW, Brown PO, 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
38. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC,SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK 2009. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326: 1112-1115
39. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CRde Leon N, Kaeppler SM, 2011. Genome-wide atlas of transcription during maize development. Plant J 66: 553-563
40. Soos V, Sebestyen E, Juhasz A, Light ME, Kohout L, Szalai G, Tandori J, Van Staden J, Balazs E, 2010. Transcriptome analysis of germinating maize kernels exposed to smoke-water and the active compound KAR1. BMC Plant Biol 10: 236
41. Spollen WG, Tao W, Valliyodan B, Chen K, Hejlek LG, Kim JJ, LeNoble ME, Zhu J, Bohnert HJ, Henderson D, Schachtman DP, Davis GE, Springer GK, Sharp RE, Nguyen HT, 2008. Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential. BMC Plant Biol 8: 32
42. Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM, 2008. Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis. BMC Plant Biol 8: 33
43. The Gene Ontology Consortium, 2000. Gene ontology: tool for the unification of biology. Nat. Genet 25(1): 25-29
44. Thiemann A, Fu J, Schrag TA, Melchinger AE, Frisch M, Scholten S, 2010. Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L. Theor Appl Genet 120(2): 401-413
45. Yue G, Zhuang Y, Li Z, Sun L, Zhang J, 2008. Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress. Biosci Rep 28(3): 125-34
46. Zhaoxia L, Changzheng X, Kunpeng L, Shi Y, Xun Q, Juren Z, 2012. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36368