DNA microarray technology and its application in fish biology and aquaculture

Frontiers of Biology in China

Volumn 4, Issue 3, 2009, Pages 305-313

  Zhang, Jianshe ^a   Chu, Wuying ^a   Fu, Guihong ^a  

^a CHANGSHA UNIVERSITY   (China)

Author keywords

Aquaculture; Bioinformatics; Complementary DNA (cDNA) microarray; Teleost fish; Transcription profiles

Indexed keywords

TELEOSTEI;

EID: 67449119196     PISSN: 16733509     EISSN: 16733622     Source Type: Journal    
DOI: 10.1007/s11515-009-0016-7     Document Type: Review

References (61)

1. A. Adams K. D. Thompson 2006 Biotechnology offers revolution to fish health management Trends Biotechnol 24 5 201 205 (Pubitemid 44308137)
2. S. L. Arcand A. M. Mes-Masson D. Provencher T. J. Hudson P. N. Tonin 2004 Gene expression microarray analysis and genome databases facilitate the characterization of a chromosome 22 derived homogeneously staining region Mol Carcinog 41 1 17 38 (Pubitemid 39195598)
3. A. D. Benninghoff D. E. Williams 2008 Identification of a transcriptional fingerprint of estrogen exposure in rainbow trout liver Toxicol Sci 101 1 65 80 (Pubitemid 350239012)
4. J. A. Berger S. Hautaniemi A. K. Jarvinen H. Edgren S. K. Mitra J. Astola 2004 Optimized LOWESS normalization parameter selection for DNA microarray data BMC Bioinformatics 5 194
5. B. M. Bolstad R. A. Irizarry M. Astrand T. P. Speed 2003 A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 19 2 185 193 (Pubitemid 36181903)
6. M. M. Brown T. D. Williams J. Kevin Chipman I. Katsiadaki M. Sanders J. A. Craft 2008 Construction of subtracted EST and normalised cDNA libraries from liver of chemical-exposed three-spined stickleback (Gasterosteus aculeatus) containing pollutant-responsive genes as a resource for transcriptome analysis Mar Environ Res 66 1 127 130
7. J. Y. Byon T. Ohira I. Hirono T. Aoki 2005 Use of a cDNA microarray to study immunity against viral hemorrhagic septicemia (VHS) in Japanese flounder (Paralichthys olivaceus) following DNA vaccination Fish Shellfish Immunol 18 2 135 147 (Pubitemid 39308560)
8. J. Y. Byon T. Ohira I. Hirono T. Aoki 2006 Comparative immune responses in Japanese flounder, Paralichthys olivaceus after vaccination with viral hemorrhagic septicemia virus (VHSV) recombinant glycoprotein and DNA vaccine using a microarray analysis Vaccine 24 7 921 930 (Pubitemid 43185308)
9. R. Cohen V. Chalifa-Caspi T. D. Williams M. Auslander S. G. George J. K. Chipman M. Tom 2007 Estimating the efficiency of fish crossspecies cDNA microarray hybridization Mar Biotechnol (NY) 9 4 491 499 (Pubitemid 47492133)
10. C. Colantuoni G. Henry S. Zeger J. Pevsner 2002 Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts Biotechniques 32 6 1316 1320 (Pubitemid 34619763)
11. M. Corredor-Adamez M. C. Welten H. P. Spaink J. E. Jeffery R. T. Schoon M.A. de Bakker C. P. Bagowski A. H. Meijer F. J. Verbeek M. K. Richardson 2005 Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a Evolution & Development 7 5 362 375 (Pubitemid 41741777)
12. M. J. Darias J. L. Zambonino-Infante K. Hugot C. L. Cahu D. Mazurais 2008 Gene expression patterns during the larval development of European sea bass (dicentrarchus labrax) by microarray analysis Mar Biotechnol (NY) 10 4 416 428
13. S. E. Douglas 2006 Microarray studies of gene expression in fish Omics 10 4 474 489 (Pubitemid 46174580)
14. M. B. Eisen P. T. Spellman P. O. Brown D. Botstein 1998 Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 95 25 14863 14868 (Pubitemid 29003722)
15. K. V. Ewart J. C. Belanger J. Williams T. Karakach S. Penny S. C. Tsoi R. C. Richards S. E. Douglas 2005 Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology Dev Comp Immunol 29 4 333 347 (Pubitemid 40017793)
16. O. Fiehn 2001 Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks Comp Funct Genomics 2 3 155 168 (Pubitemid 32590962)
17. E. F. Finne G. A. Cooper B. F. Koop K. Hylland K. E. Tollefsen 2007 Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture Aquat Toxicol 81 3 293 303 (Pubitemid 46273699)
18. T. Fujimoto M. Koyanagi I. Baba K. Nakabayashi N. Kato T. Sasazuki S. Shirasawa 2007 Analysis of KRAP expression and localization, and genes regulated by KRAP in a human colon cancer cell line J Hum Genet 52 12 978 984 (Pubitemid 350164615)
19. S. F. Gonzalez M. J. Krug M. E. Nielsen Y. Santos D. R. Call 2004 Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray J Clin Microbiol 42 4 1414 1419 (Pubitemid 38500774)
20. A. Y. Gracey 2007 Interpreting physiological responses to environmental change through gene expression profiling J Exp Biol 210 Pt9 1584 1592 (Pubitemid 46841963)
21. M. Hirayama M. N. Ahsan H. Mitani S. Watabe 2008 CYR61 is a novel gene associated with temperature-dependent changes in fish metabolism as revealed by cDNA microarray analysis on a medaka Oryzias latipes cell line J Cell Biochem 104 4 1297 1310 (Pubitemid 351961702)
22. Z. Ju R. A. Dunham Z. Liu 2002 Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation Mol Genet Genomics 268 1 87 95
23. Z. Ju M. C. Wells S. J. Heater R. B. Walter 2007 Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia Comp Biochem Physiol C Toxicol Pharmacol 145 1 134 144 (Pubitemid 46210199)
24. Z. Ju M. C. Wells R. B. Walter 2007 DNA microarray technology in toxicogenomics of aquatic models: methods and applications Comp Biochem Physiol C Toxicol Pharmacol 145 1 5 14 (Pubitemid 46210198)
25. K. S. Kassahn M. J. Caley A. C. Ward A. R. Connolly G. Stone R. H. Crozier 2007 Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish Mol Ecol 16 8 1749 1763 (Pubitemid 46525383)
26. Katogi R, Nakatani Y, Shini T, Kohara Y, Inohaya K, Kudo A (2004). Large-scale analysis of the genes involved in fin regeneration and blastema formation in the medaka, Oryzias latipes. Mech Dev, 121 (7-8): 861-872 (Pubitemid 38813142)
27. M. Kochzius M. Nolte H. Weber N. Silkenbeumer S. Hjorleifsdottir G. O. Hreggvidsson V. Marteinsson K. Kappel S. Planes F. Tinti A. Magoulas E. Garcia Vazquez C. Turan C. Hervet D. Campo Falgueras A. Antoniou M. Landi D. Blohm 2008 DNA microarrays for identifying fishes Mar Biotechnol (NY) 10 2 207 217
28. H. Koskinen P. Pehkonen E. Vehniainen A. Krasnov C. Rexroad S. Afanasyev H. Molsa A. Oikari 2004 Response of rainbow trout transcriptome to model chemical contaminants Biochem Biophys Res Commun 320 3 745 753 (Pubitemid 38887206)
29. T. Kurobe M. Yasuike T. Kimura I. Hirono T. Aoki 2005 Expression profiling of immune-related genes from Japanese flounder Paralichthys olivaceus kidney cells using cDNA microarrays Dev Comp Immunol 29 6 515 523 (Pubitemid 40326988)
30. S. H. Lam Z. Gong 2006 Modeling liver cancer using zebrafish: a comparative oncogenomics approach Cell Cycle 5 6 573 577
31. S. H. Lam C. L. Winata Y. Tong S. Korzh W. S. Lim V. Korzh J. Spitsbergen S. Mathavan L. D. Miller E. T. Liu Z. Gong 2006 Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver Physiol Genomics 27 3 351 361 (Pubitemid 46708786)
32. P. Larkin D. L. Villeneuve I. Knoebl A. L. Miracle B. J. Carter L. Liu N. D. Denslow G. T. Ankley 2007 Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas) Environ Toxicol Chem 26 7 1497 1506 (Pubitemid 47067333)
33. Y. F. Leung P. Ma J. E. Dowling 2007 Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo Invest Ophthalmol Vis Sci 48 2 881 890 (Pubitemid 351260726)
34. C. L. Lien M. Schebesta S. Makino G. J. Weber M. T. Keating 2006 Gene expression analysis of zebrafish heart regeneration PLoS Biol 4 8 e260
35. E. Linney B. Dobbs-McAuliffe H. Sajadi R. L. Malek 2004 Microarray gene expression profiling during the segmentation phase of zebrafish development Comp Biochem Physiol C Toxicol Pharmacol 138 3 351 362 (Pubitemid 39469070)
36. E. Linney L. Upchurch S. Donerly 2004 Zebrafish as a neurotoxicological model Neurotoxicol Teratol 26 6 709 718 (Pubitemid 39296754)
37. J. Lo S. Lee M. Xu F. Liu H. Ruan A. Eun Y. He W. Ma W. Wang Z. Wen J. Peng 2003 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis Genome Res 13 3 455 466 (Pubitemid 36395403)
38. D. T. Lua M. Yasuike I. Hirono T. Aoki 2005 Transcription program of red sea bream iridovirus as revealed by DNA microarrays J Virol 79 24 15151 15164 (Pubitemid 43032298)
39. S. A. Martin S. C. Blaney D. F. Houlihan C. J. Secombes 2006 Transcriptome response following administration of a live bacterial vaccine in Atlantic salmon (Salmo salar) Mol Immunol 43 11 1900 1911
40. C. J. Martyniuk E. R. Gerrie J. T. Popesku M. Ekker V. L. Trudeau 2007 Microarray analysis in the zebrafish (Danio rerio) liver and telencephalon after exposure to low concentration of 17alpha-ethinylestradiol Aquat Toxicol 84 1 38 49 (Pubitemid 47096745)
41. A. H. Meijer F. J. Verbeek E. Salas-Vidal M. Corredor-Adamez J. Bussman A. M. van der Sar G. W. Otto R. Geisler H. P. Spaink 2005 Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection Mol Immunol 42 10 1185 1203
42. L. N. Moens R. Smolders K. van der Ven P. van Remortel J. Del-Favero W. M. De Coen 2007 Effluent impact assessment using microarraybased analysis in common carp: a systems toxicology approach Chemosphere 67 11 2293 2304 (Pubitemid 46441392)
43. L. N. Moens K. van der Ven P. Van Remortel J. Del-Favero W. M. De Coen 2007 Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray J Biochem Mol Toxicol 21 5 299 311 (Pubitemid 350006287)
44. M. Nishidate Y. Nakatani A. Kudo A. Kawakami 2007 Identification of novel markers expressed during fin regeneration by microarray analysis in medaka fish Dev Dyn 236 9 2685 2693 (Pubitemid 47450958)
45. A. E. Oostlander G. A. Meijer B. Ylstra 2004 Microarray-based comparative genomic hybridization and its applications in human genetics Clin Genet 66 6 488 495 (Pubitemid 39562010)
46. J. R. Pollack C. M. Perou A. A. Alizadeh M. B. Eisen A. Pergamenschikov C. F. Williams S. S. Jeffrey D. Botstein P. O. Brown 1999 Genome-wide analysis of DNA copy-number changes using cDNA microarrays Nat Genet 23 1 41 46 (Pubitemid 29418785)
47. T. Ranheim M. Mattingsdal J. M. Lindvall O. L. Holla K. E. Berge M. A. Kulseth T. P. Leren 2008 Genome-wide expression analysis of cells expressing gain of function mutant D374Y-PCSK9 J Cell Physiol 217 2 459 467
48. S. C. Renn N. Aubin-Horth H. A. Hofmann 2004 Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray BMC Genomics 5 1 42
49. M. L. Rise S. R. Jones G. D. Brown K. R. von Schalburg W. S. Davidson B. F. Koop 2004 Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection Physiol Genomics 20 1 21 35
50. M. Salem P. B. Kenney C. E. Rexroad 3rd J. Yao 2006 Microarray gene expression analysis in atrophying rainbow trout muscle: a unique nonmammalian muscle degradation model Physiol Genomics 281 33 45 (Pubitemid 46702015)
51. M. Schebesta C. L. Lien F. B. Engel M. T. Keating 2006 Transcriptional profiling of caudal fin regeneration in zebrafish Sci World J 6 38 54 (Pubitemid 46155752)
52. C. Ton D. Stamatiou V. J. Dzau C. C. Liew 2002 Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development Biochem Biophys Res Commun 296 5 1134 1142
53. C. Ton D. Stamatiou C. C. Liew 2003 Gene expression profile of zebrafish exposed to hypoxia during development Physiol Genomics 13 2 97 106 (Pubitemid 37129174)
54. S. C. Tsoi J. M. Cale I. M. Bird V. Ewart L. L. Brown S. Douglas 2003 Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection Mar Biotechnol (NY) 5 6 545 554 (Pubitemid 38106639)
55. D. L. van der Meer G. E. van den Thillart F. Witte M. A. de Bakker J. Besser M. K. Richardson H. P. Spaink J. T. Leito C. P. Bagowski 2005 Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish Am J Physiol Regul Integr Comp Physiol 289 5 R1512 1519
56. K. van der Ven M. De Wit D. Keil L. Moens K. van Leemput B. Naudts W. De Coen 2005 Development and application of a brain-specific cDNA microarray for effect evaluation of neuro-active pharmaceuticals in zebrafish (Danio rerio) Comp Biochem Physiol B Biochem Mol Biol 141 4 408 417 (Pubitemid 40982000)
57. T. D. Williams K. Gensberg S. D. Minchin J. K. Chipman 2003 A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus) Aquat Toxicol 65 2 141 157 (Pubitemid 37011308)
58. W. Wu X. Liu M. Xu J. R. Peng R. Setiono 2005 A hybrid SOM-SVM approach for the zebrafish gene expression analysis Genomics Proteomics Bioinformatics 3 2 84 93 (Pubitemid 43014132)
59. C. C. Xiang Y. Chen 2000 cDNA microarray technology and its applications Biotechnol Adv 18 1 35 46 (Pubitemid 30300756)
60. Y. H. Yang M. J. Buckley T. P. Speed 2001 Analysis of cDNA microarray images Brief Bioinform 2 4 341 349
61. D. Zhang M. T. Wells C. D. Smart W. E. Fry 2005 Bayesian normalization and identification for differential gene expression data J Comput Biol 12 4 391 406 (Pubitemid 40696478)