Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Pinto, Patrícia I S ^a   Matsumura, Hideo ^b   Thorne, Michael A S ^c   Power, Deborah M ^a   Terauchi, Ryohei ^d   Reinhardt, Richard ^e   Canário, Adelino V M ^a  

^a UNIVERSITY OF ALGARVE   (Portugal)

^b SHINSHU UNIVERSITY   (Japan)

^c BRITISH ANTARCTIC SURVEY   (United Kingdom)

^d IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

^e MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; COMPLEMENTARY DNA; CYTOSKELETON PROTEIN; GENOMIC DNA; POTASSIUM ION; TRANSCRIPTOME; WATER; CALCIUM; CALCIUM CHANNEL; DNA; FISH PROTEIN; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CALCIUM HOMEOSTASIS; ENERGY METABOLISM; ENVIRONMENTAL CHANGE; GENE MAPPING; GILL; MOLECULAR GENETICS; MUSCLE CONTRACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PUFFER FISH; RNA TRANSCRIPTION; SALINITY; SERIAL ANALYSIS OF GENE EXPRESSION; SIGNAL TRANSDUCTION; TELEOST; ANIMAL; BLOOD; CHEMISTRY; CLUSTER ANALYSIS; DOWN REGULATION; DRUG EFFECT; ENVIRONMENT; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC DATABASE; GENETICS; METABOLISM; PIGMENTATION; POLYMERASE CHAIN REACTION; TETRAODONTIFORMES; TIME; UPREGULATION;

TELEOSTEI; TETRAODON NIGROVIRIDIS; TETRAODONTIDAE;

ANIMALS; CALCIUM; CALCIUM CHANNELS; CLUSTER ANALYSIS; DATABASES, GENETIC; DNA; DOWN-REGULATION; ENVIRONMENT; EXPRESSED SEQUENCE TAGS; FISH PROTEINS; GENE EXPRESSION PROFILING; GENE LIBRARY; GILLS; MOLECULAR SEQUENCE ANNOTATION; PIGMENTATION; POLYMERASE CHAIN REACTION; RNA, MESSENGER; TETRAODONTIFORMES; TIME FACTORS; UP-REGULATION; WATER;

EID: 77955523888     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-476     Document Type: Article

References (89)

1. Wendelaar Bonga SE, Pang PK. Control of calcium regulating hormones in the vertebrates: parathyroid hormone, calcitonin, prolactin, and stanniocalcin. Int Rev Cytol 1991, 128:139-213.
2. Hoenderop JGJ, Nilius B, Bindels RJM. Calcium absorption across epithelia. Physiol Rev 2005, 85:373-422. 10.1152/physrev.00003.2004, 15618484.
3. Guerreiro PM, Fuentes J. Control of calcium balance in fish. Fish Osmoregulation 2007, Enfield, USA: Science Publishers, Baldisserotto B, Mancera Romero JM, Kapoor BG.
4. Abbink W, Bevelander GS, Hang X, Lu W, Guerreiro PM, Spanings T, Canario AV, Flik G. PTHrP regulation and calcium balance in sea bream (Sparus auratus L.) under calcium constraint. J Exp Biol 2006, 209:3550-3557. 10.1242/jeb.02399, 16943495.
5. Abbink W, Bevelander GS, Rotllant J, Canario AV, Flik G. Calcium handling in Sparus auratus: effects of water and dietary calcium levels on mineral composition, cortisol and PTHrP levels. J Exp Biol 2004, 207:4077-4084. 10.1242/jeb.01254, 15498953.
6. Flik G, Fenwick JC, Kolar Z, Mayer-Gostan N, Wendelaabonga SE. Effects of low ambient calcium levels on wholebody Ca2+ flux rates and internal calcium pools in the freshwater cichlid teleost, Oreochromis Mossambicus. J Exp Biol 1986, 120:249-264.
7. Guerreiro PM, Fuentes J, Flik G, Rotllant J, Power DM, Canario AV. Water calcium concentration modifies whole-body calcium uptake in sea bream larvae during short-term adaptation to altered salinities. J Exp Biol 2004, 207:645-653. 10.1242/jeb.00765, 14718507.
8. Evans DH, Piermarini PM, Choe KP. The multifunctional fish gill: dominant site of gas exchange, osmoregulation, acid-base regulation, and excretion of nitrogenous waste. Physiol Rev 2005, 85:97-177. 10.1152/physrev.00050.2003, 15618479.
9. Flik G, Verbost PM, Wendelaar Bongar SE. Calcium transport process in fishes. Cellular and Molecular Approaches to Fish Ionic Regulation 1995, San Diego, CA: Academic, Wood C, Shuttleworth T.
10. Liao BK, Deng AN, Chen SC, Chou MY, Hwang PP. Expression and water calcium dependence of calcium transporter isoforms in zebrafish gill mitochondrion-rich cells. BMC Genomics 2007, 8:354. 10.1186/1471-2164-8-354, 2140269, 17915033.
11. Shahsavarani A, Perry SF. Hormonal and environmental regulation of the epithelial calcium channel (ECaC) in the gill of rainbow trout (Oncorhynchus mykiss). Am J Physiol Regul Integr Comp Physiol 2006, 291:R1490-1498.
12. Craig PM, Wood CM, McClelland GB. Gill membrane remodeling with soft-water acclimation in zebrafish (Danio rerio). Physiol Genomics 2007, 30:53-60. 10.1152/physiolgenomics.00195.2006, 17299134.
13. Pan TC, Liao BK, Huang CJ, Lin LY, Hwang PP. Epithelial Ca2+ channel expression and Ca2+ uptake in developing zebrafish. Am J Physiol Regul Integr Comp Physiol 2005, 289:R1202-1211.
14. Fiol DF, Kultz D. Osmotic stress sensing and signaling in fishes. Febs J 2007, 274:5790-5798. 10.1111/j.1742-4658.2007.06099.x, 17944942.
15. Abbink W, Flik G. Parathyroid hormone-related protein in teleost fish. Gen Comp Endocrinol 2007, 152:243-251. 10.1016/j.ygcen.2006.11.010, 17188690.
16. Loretz CA. Extracellular calcium-sensing receptors in fishes. Comp Biochem Physiol A Mol Integr Physiol 2008, 149:225-245. 10.1016/j.cbpa.2008.01.037, 18302989.
17. Wagner G, Dimattia G. The stanniocalcin family of proteins. J Exp Zool A Comp Exp Biol 2006, 305:769-780.
18. Tetraodon nigroviridis. , http://www.fishbase.org
19. Lin CH, Tsai RS, Lee TH. Expression and distribution of Na, K-ATPase in gill and kidney of the spotted green pufferfish, Tetraodon nigroviridis, in response to salinity challenge. Comp Biochem Physiol A Mol Integr Physiol 2004, 138:287-295. 10.1016/j.cbpb.2004.04.005, 15313482.
20. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431:946-957. 10.1038/nature03025, 15496914.
21. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science 1995, 270:484-487. 10.1126/science.270.5235.484, 7570003.
22. Matsumura H, Kruger DH, Kahl G, Terauchi R. SuperSAGE: a modern platform for genome-wide quantitative transcript profiling. Curr Pharm Biotechnol 2008, 9:368-374. 10.2174/138920108785915157, 18855689.
23. Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci USA 2003, 100:15718-15723. 10.1073/pnas.2536670100, 307634, 14676315.
24. Terauchi R, Matsumura H, Kruger DH, Kahl G. SuperSAGE: the most advanced transcriptome technology for functional genomics. Handbook of Plant Functional Genomics: Concepts and Protocols 2008, 37-54. New York: John Wiley & Sons, Kahl G, Meksem K.
25. Greenwood MP, Flik G, Wagner GF, Balment RJ. The corpuscles of Stannius, calcium-sensing receptor, and stanniocalcin: responses to calcimimetics and physiological challenges. Endocrinology 2009, 150:3002-3010. 10.1210/en.2008-1758, 2703514, 19299449.
26. Wang SM. Understanding SAGE data. Trends Genet 2007, 23:42-50. 10.1016/j.tig.2006.11.001, 17109989.
27. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31:28-33. 10.1093/nar/gkg033, 165480, 12519941.
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
29. Loh YH, Christoffels A, Brenner S, Hunziker W, Venkatesh B. Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes. Genome Res 2004, 14:1248-1257. 10.1101/gr.2400004, 442139, 15197168.
30. Kalujnaia S, McWilliam IS, Zaguinaiko VA, Feilen AL, Nicholson J, Hazon N, Cutler CP, Balment RJ, Cossins AR, Hughes M, Cramb G. Salinity adaptation and gene profiling analysis in the European eel (Anguilla anguilla) using microarray technology. Gen Comp Endocrinol 2007, 152:274-280. 10.1016/j.ygcen.2006.12.025, 17324422.
31. Evans TG, Somero GN. A microarray-based transcriptomic time-course of hyper- and hypo-osmotic stress signaling events in the euryhaline fish Gillichthys mirabilis: osmosensors to effectors. J Exp Biol 2008, 211:3636-3649. 10.1242/jeb.022160, 18978229.
32. Kalujnaia S, McWilliam IS, Zaguinaiko VA, Feilen AL, Nicholson J, Hazon N, Cutler CP, Cramb G. Transcriptomic approach to the study of osmoregulation in the European eel Anguilla anguilla. Physiol Genomics 2007, 31:385-401. 10.1152/physiolgenomics.00059.2007, 17666525.
33. Boutet I, Long Ky CL, Bonhomme F. A transcriptomic approach of salinity response in the euryhaline teleost, Dicentrarchus labrax. Gene 2006, 379:40-50. 10.1016/j.gene.2006.04.011, 16737785.
34. Kultz D, Fiol D, Valkova N, Gomez-Jimenez S, Chan SY, Lee J. Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms. J Exp Biol 2007, 210:1593-1601. 10.1242/jeb.000141, 17449824.
35. Hwang P-P, Tung Y-C, Chang M-H. Effect of environmental calcium levels on calcium uptake in tilapia larvae Oreochromis mossambicus. Fish Physiol Biochem 1996, 15:363-370.
36. Chen YY, Lu FI, Hwang PP. Comparisons of calcium regulation in fish larvae. J Exp Zool A Comp Exp Biol 2003, 295:127-135. 10.1002/jez.a.10195, 12541296.
37. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Kinzler KW. Analysis of human transcriptomes. Nat Genet 1999, 23:387-388. 10.1038/70487, 10581018.
38. Matsumura H, Ito A, Saitoh H, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R. SuperSAGE, Technoreview. Cell Microbiol 2005, 7:11-18. 10.1111/j.1462-5822.2004.00478.x, 15617519.
39. Molina C, Rotter B, Horres R, Udupa SM, Besser B, Bellarmino L, Baum M, Matsumura H, Terauchi R, Kahl G, Winter P. SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 2008, 9:553. 10.1186/1471-2164-9-553, 2628679, 19025623.
40. Zhu J, He F, Wang J, Yu J. Modeling transcriptome based on transcript-sampling data. PLoS One 2008, 3:e1659. 10.1371/journal.pone.0001659, 2243018, 18286206.
41. Schaaf GJ, Ruijter JM, van Ruissen F, Zwijnenburg DA, Waaijer R, Valentijn LJ, Benit-Deekman J, van Kampen AH, Baas F, Kool M. Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J 2005, 19:404-406.
42. Keime C, Damiola F, Mouchiroud D, Duret L, Gandrillon O. Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics 2004, 5:143. 10.1186/1471-2105-5-143, 535903, 15469608.
43. Liang P. SAGE Genie: a suite with panoramic view of gene expression. Proc Natl Acad Sci USA 2002, 99:11547-11548. 10.1073/pnas.192436299, 129301, 12195021.
44. Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF. SAGEmap: a public gene expression resource. Genome Res 2000, 10:1051-1060. 10.1101/gr.10.7.1051, 310889, 10899154.
45. Boon W-M, Beissbarth T, Hyde L, Smyth G, Gunnersen J, Denton DA, Scott H, Tan S-S. A comparative analysis of transcribed genes in the mouse hypothalamus and neocortex reveals chromosomal clustering. Proc Natl Acad Sci USA 2004, 101:14972-14977. 10.1073/pnas.0406296101, 522044, 15466702.
46. Calsa T, Figueira A. Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. Plant Mol Biol 2007, 63:745-762. 10.1007/s11103-006-9121-z, 17211512.
47. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJ, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol 2008, 9:R99. 10.1186/gb-2008-9-6-r99, 2481431, 18554416.
48. Perry SF, Wood CM. Kinetics of branchial calcium uptake in the rainbow trout: effects of acclimation to various external calcium levels. J Exp Biol 1985, 116:411-433.
49. Katoh F, Kaneko T. Effects of environmental Ca2+ levels on branchial chloride cell morphology in freshwater-adapted killifish Fundulus heteroclitus. Fisheries Sci 2002, 68:347-355.
50. Laurent P, Hobe H, Dunel-Erb S. The role of environmental sodium chloride relative to calcium in gill morphology of freshwater salmonid fish. Cell Tissue Res 1985, 240:675-692.
51. Chang IC, Lee TH, Yang CH, Wei YY, Chou FI, Hwang PP. Morphology and function of gill mitochondria-rich cells in fish acclimated to different environments. Physiol Biochem Zool 2001, 74:111-119. 10.1086/319304, 11226019.
52. Uchida K, Hasegawa S, Kaneko T. Effects of a low-Ca2+ environment on branchial chloride cell morphology in chum salmon fry and immunolocalization of Ca2+-ATPase in chloride cells. Can J Zool 2002, 80:1100-1108.
53. Daborn K, Cozzi RR, Marshall WS. Dynamics of pavement cell-chloride cell interactions during abrupt salinity change in Fundulus heteroclitus. J Exp Biol 2001, 204:1889-1899.
54. Coemans B, Matsumura H, Terauchi R, Remy S, Swennen R, Sagi L. SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism. Theor Appl Genet 2005, 111:1118-1126. 10.1007/s00122-005-0039-7, 16133315.
55. Tang Z, Li Y, Wan P, Li X, Zhao S, Liu B, Fan B, Zhu M, Yu M, Li K. LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol 2007, 8:R115. 10.1186/gb-2007-8-6-r115, 2394763, 17573972.
56. Ling K-H, Hewitt C, Beissbarth T, Hyde L, Banerjee K, Cheah P-S, Cannon P, Hahn C, Thomas P, Smyth G, Tan S-S, Thomas T, Scott H. Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biol 2009, 10:R104. 10.1186/gb-2009-10-10-r104, 2784319, 19799774.
57. Tsai JC, Hwang PP. Effects of wheat germ agglutinin and colchicine on microtubules of the mitochondria-rich cells and Ca2+ uptake in tilapia (Oreochromis mossambicus) larvae. J Exp Biol 1998, 201:2263-2271.
58. Nilsson S. Filament position in fish gills is influenced by a smooth muscle innervated by adrenergic nerves. J Exp Biol 1985, 118:433-437.
59. Arif SH. A Ca2+-binding protein with numerous roles and uses: parvalbumin in molecular biology and physiology. Bioessays 2009, 31:410-421. 10.1002/bies.200800170, 19274659.
60. de Groof AJ, Fransen JA, Errington RJ, Willems PH, Wieringa B, Koopman WJ. The creatine kinase system is essential for optimal refill of the sarcoplasmic reticulum Ca2+ store in skeletal muscle. J Biol Chem 2002, 277:5275-5284. 10.1074/jbc.M108157200, 11734556.
61. Puzianowska-Kuznicka M, Kuznicki J. The ER and ageing II: calcium homeostasis. Ageing Res Rev 2009, 8:160-172. 10.1016/j.arr.2009.05.002, 19427411.
62. Perry SF. The chloride cell: structure and function in the gills of freshwater fishes. Annu Rev Physiol 1997, 59:325-347. 10.1146/annurev.physiol.59.1.325, 9074767.
63. Porta AR, Bettini E, Buiakova OI, Baker H, Danho W, Margolis FL. Molecular cloning of ictacalcin: A novel calcium-binding protein from the channel catfish, Ictalurus punctatus. Mol Brain Res 1996, 41:81-89. 10.1016/0169-328X(96)00069-1, 8883937.
64. Loretz CA, Pollina C, Hyodo S, Takei Y. Extracellular calcium-sensing receptor distribution in osmoregulatory and endocrine tissues of the tilapia. Gen Comp Endocrinol 2009, 161:216-228. 10.1016/j.ygcen.2008.12.020, 19523399.
65. Haeseleer F, Imanishi Y, Sokal I, Filipek S, Palczewski K. Calcium-binding proteins: intracellular sensors from the calmodulin superfamily. Biochem Biophys Res Commun 2002, 290:615-623. 10.1006/bbrc.2001.6228, 11785943.
66. Santamaria-Kisiel L, Rintala-Dempsey AC, Shaw GS. Calcium-dependent and -independent interactions of the S100 protein family. Biochem J 2006, 396:201-214. 10.1042/BJ20060195, 1462724, 16683912.
67. Penniston JT, Enyedi A. Modulation of the plasma membrane Ca2+ pump. J Membr Biol 1998, 165:101-109. 10.1007/s002329900424, 9744998.
68. Vanagas L, Rossi RC, Caride AJ, Filoteo AG, Strehler EE, Rossi JP. Plasma membrane calcium pump activity is affected by the membrane protein concentration: evidence for the involvement of the actin cytoskeleton. Biochim Biophys Acta 2007, 1768:1641-1649. 10.1016/j.bbamem.2007.03.012, 2041878, 17481573.
69. Bagherie-Lachidan M, Wright SI, Kelly SP. Claudin-3 tight junction proteins in Tetraodon nigroviridis: cloning, tissue-specific expression, and a role in hydromineral balance. Am J Physiol Regul Integr Comp Physiol 2008, 294:R1638-1647.
70. Bagherie-Lachidan M, Wright SI, Kelly SP. Claudin-8 and -27 tight junction proteins in puffer fish Tetraodon nigroviridis acclimated to freshwater and seawater. J Comp Physiol B 2009, 179:419-431. 10.1007/s00360-008-0326-0, 19112569.
71. Tipsmark CK, Baltzegar DA, Ozden O, Grubb BJ, Borski RJ. Salinity regulates claudin mRNA and protein expression in the teleost gill. Am J Physiol Regul Integr Comp Physiol 2008, 294:R1004-1014.
72. Tipsmark CK, Kiilerich P, Nilsen TO, Ebbesson LO, Stefansson SO, Madsen SS. Branchial expression patterns of claudin isoforms in Atlantic salmon during seawater acclimation and smoltification. Am J Physiol Regul Integr Comp Physiol 2008, 294:R1563-1574.
73. Tipsmark CK, Luckenbach JA, Madsen SS, Kiilerich P, Borski RJ. Osmoregulation and expression of ion transport proteins and putative claudins in the gill of southern flounder (Paralichthys lethostigma). Comp Biochem Physiol A Mol Integr Physiol 2008, 150:265-273. 10.1016/j.cbpa.2008.03.006, 18467139.
74. Giffard-Mena I, Boulo V, Aujoulat F, Fowden H, Castille R, Charmantier G, Cramb G. Aquaporin molecular characterization in the sea-bass (Dicentrarchus labrax): the effect of salinity on AQP1 and AQP3 expression. Comp Biochem Physiol A Mol Integr Physiol 2007, 148:430-444. 10.1016/j.cbpa.2007.06.002, 17618150.
75. Cutler CP, Martinez AS, Cramb G. The role of aquaporin 3 in teleost fish. Comp Biochem Physiol A Mol Integr Physiol 2007, 148:82-91. 10.1016/j.cbpa.2006.09.022, 17126580.
76. ASAB Guidelines for the treatment of animals in behavioural research and teaching. Anim Behav 2003, 65:249-255. ASAB.
77. Matsumura H, Reuter M, Kruger DH, Winter P, Kahl G, Terauchi R. SuperSAGE. Methods Mol Biol 2008, 387:55-70.
78. The Gene Expression Omnibus (GEO) repository. , http://www.ncbi.nlm.nih.gov/geo
79. Schaaf GJ, van Ruissen F, van Kampen A, Kool M, Ruijter JM. Statistical comparison of two or more SAGE libraries: one tag at a time. Methods Mol Biol 2008, 387:151-168.
80. Kal AJ, van Zonneveld AJ, Benes V, van den Berg M, Koerkamp MG, Albermann K, Strack N, Ruijter JM, Richter A, Dujon B, Ansorge W, Tabak HF. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol Biol Cell 1999, 10:1859-1872. 25383, 10359602.
81. NCBI FTP directory for BLAST executables. , ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/
82. NCBI GenBank. , http://www.ncbi.nlm.nih.gov/Genbank/
83. Ensembl anonymous FTP site- Tetraodon nigroviridis cDNAs. , ftp://ftp.ensembl.org/pub/current_fasta/tetraodon_nigroviridis/cdna/
84. The Tetraodon nigroviridis genome (Assembly 8, Golden Path v.2, March 2007). , http://www.genoscope.cns.fr/externe/Download/Projets/Projet_C/genomique/goldenpath_v2/unmasked/
85. Uniprot FTP repository. , ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase
86. Kim K, Zhang S, Jiang K, Cai L, Lee IB, Feldman LJ, Huang H. Measuring similarities between gene expression profiles through new data transformations. BMC Bioinformatics 2007, 8:29. 10.1186/1471-2105-8-29, 1804284, 17257435.
87. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 1995, 57:289-300.
88. Cikos S, Bukovska A, Koppel J. Relative quantification of mRNA: comparison of methods currently used for real-time PCR data analysis. BMC Mol Biol 2007, 8:113. 10.1186/1471-2199-8-113, 2235892, 18093344.
89. Uniprot. , http://www.uniprot.org/