Probing the Xenopus laevis inner ear transcriptome for biological function

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Powers, TuShun R ^a   Virk, Selene M ^a   Trujillo Provencio, Casilda ^a   Serrano, Elba E ^a  

^a NEW MEXICO STATE UNIVERSITY   (United States)

Author keywords

Amphibian; Auditory; Deafness; Hearing; Microarray; Organ; Vestibular

Indexed keywords

ION CHANNEL; TRANSCRIPTION FACTOR;

ARTICLE; BIOINFORMATICS; BIOLOGICAL FUNCTIONS; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE IDENTIFICATION; GENE PROBE; GENE TARGETING; GENETIC ASSOCIATION; GENOME; HEARING; HEARING IMPAIRMENT; INNER EAR; ION TRANSPORT; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; SPECIES COMPARISON; VESTIBULAR FUNCTION; XENOPUS LAEVIS;

AMINO ACID SEQUENCE; AMPHIBIAN PROTEINS; ANIMALS; DNA, COMPLEMENTARY; EAR, INNER; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME; HUMANS; MECHANOTRANSDUCTION, CELLULAR; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TRANSCRIPTOME; XENOPUS LAEVIS;

AMPHIBIA; ANIMALIA; XENOPUS LAEVIS;

EID: 84861925316     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-225     Document Type: Article

References (96)

1. WHO Deafness and hearing impairment [http://www.who.int/mediacentre/factsheets/fs300/en/], WHO.
2. Statistics- Vestibular Disorders Association Vertigo, Imbalance, Dizziness resources [http://www.vestibular.org/vestibular-disorders/statistics.php], Statistics- Vestibular Disorders Association.
3. Agrawal Y, Carey J, Della Santina C, Schubert M, Minor L. Disorders of balance and vestibular function in US adults: data from the National Health and Nutrition Examination Survey, 2001-2004. Arch Intern Med 2009, 169(10):938-944. 10.1001/archinternmed.2009.66, 19468085.
4. Quick Statistics (NIDCD Health Information)
5. Holley M. Keynote review: The auditory system, hearing loss and potential targets for drug development. Drug Discov Today 2005, 10(19):1269-1282. 10.1016/S1359-6446(05)03595-6, 16214671.
6. Staecker H, Praetorius M, Brough DE. Development of gene therapy for inner ear disease: Using bilateral vestibular hypofunction as a vehicle for translational research. Hear Res 2011, 276(1-2):44-51. 3109124, 21251965.
7. Hudspeth A. How the ear's works work. Nature 1989, 341(6241):397-404. 10.1038/341397a0, 2677742.
8. Simmons DD, Meenderink SWF, Vassilakis PN. Anatomy, physiology, and function of auditory end-organs in the frog inner ear. Hearing and Sound Communication in Amphibians 2006, 184-220. Springer, New York, Narins ASF PM, Fay RR, Popper AN.
9. Heller S. Molecular screens for inner ear genes. J Neurobiol 2002, 53(2):265-275. 10.1002/neu.10122, 12382280.
10. Forge A, Wright T. The molecular architecture of the inner ear. Br Med Bull 2002, 63:5-24. 10.1093/bmb/63.1.5, 12324381.
11. Riley B, Phillips B. Ringing in the new ear: resolution of cell interactions in otic development. Dev Biol 2003, 261(2):289-312. 10.1016/S0012-1606(03)00245-8, 14499642.
12. Fettiplace R. Active hair bundle movements in auditory hair cells. J Physiol 2006, 576(Pt 1):29-36. 1995638, 16887874.
13. Harris J, Cheng A, Cunningham L, MacDonald G, Raible D, Rubel E. Neomycin-induced hair cell death and rapid regeneration in the lateral line of zebrafish (Danio rerio). J Assoc Res Otolaryngol 2003, 4(2):219-234. 10.1007/s10162-002-3022-x, 3202713, 12943374.
14. Brignull H, Raible D, Stone J. Feathers and fins: non-mammalian models for hair cell regeneration. Brain Res 2009, 1277:12-23. 2700174, 19245801.
15. Smotherman M, Narins P. Hair cells, hearing and hopping: a field guide to hair cell physiology in the frog. J Exp Biol 2000, 203(Pt 15):2237-2246.
16. Roberts W, Howard J, Hudspeth A. Hair cells: transduction, tuning, and transmission in the inner ear. Annu Rev Cell Biol 1988, 4:63-92. 10.1146/annurev.cb.04.110188.000431, 2461723.
17. Morton C. Genetics, genomics and gene discovery in the auditory system. Hum Mol Genet 2002, 11(10):1229-1240. 10.1093/hmg/11.10.1229, 12015283.
18. Alsaber R, Tabone CJ, Kandpal RP. Predicting candidate genes for human deafness disorders: a bioinformatics approach. BMC Genomics 2006, 7:180. 10.1186/1471-2164-7-180, 1564145, 16854223.
19. Petit C. From deafness genes to hearing mechanisms: harmony and counterpoint. Trends Mol Med 2006, 12(2):57-64. 10.1016/j.molmed.2005.12.006, 16406841.
20. Raviv D, Dror AA, Avraham KB. Hearing loss: a common disorder caused by many rare alleles. Ann N Y Acad Sci 2010, 1214:168-179. 10.1111/j.1749-6632.2010.05868.x, 21175685.
21. Petersen M, Willems P. Non-syndromic, autosomal-recessive deafness. Clin Genet 2006, 69(5):371-392. 10.1111/j.1399-0004.2006.00613.x, 16650073.
22. Resendes BL, Robertson NG, Szustakowski JD, Resendes RJ, Weng Z, Morton CC. Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences. J Assoc Res Otolaryngol 2002, 3(1):45-53. 10.1007/s101620020005, 3202364, 12083723.
23. Chen ZY, Corey DP. An inner ear gene expression database. J Assoc Res Otolaryngol 2002, 3(2):140-148. 10.1007/s101620020029, 3202398, 12162364.
24. Lin J, Ozeki M, Javel E, Zhao Z, Pan W, Schlentz E, Levine S. Identification of gene expression profiles in rat ears with cDNA microarrays. Hear Res 2003, 175(1-2):2-13.
25. Morris KA, Snir E, Pompeia C, Koroleva IV, Kachar B, Hayashizaki Y, Carninci P, Soares MB, Beisel KW. Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. J Assoc Res Otolaryngol 2005, 6(1):75-89. 10.1007/s10162-004-5046-x, 2504641, 15735932.
26. Hawkins RD, Bashiardes S, Helms CA, Hu L, Saccone NL, Warchol ME, Lovett M. Gene expression differences in quiescent versus regenerating hair cells of avian sensory epithelia: implications for human hearing and balance disorders. Hum Mol Genet 2003, 12(11):1261-1272. 10.1093/hmg/ddg150, 12761041.
27. Hawkins RD, Bashiardes S, Powder KE, Sajan SA, Bhonagiri V, Alvarado DM, Speck J, Warchol ME, Lovett M. Large scale gene expression profiles of regenerating inner ear sensory epithelia. PLoS One 2007, 2(6):e525. 10.1371/journal.pone.0000525, 1888727, 17565378.
28. McDermott BJ, Baucom J, Hudspeth A. Analysis and functional evaluation of the hair-cell transcriptome. Proc Natl Acad Sci USA 2007, 104(28):11820-11825. 10.1073/pnas.0704476104, 1905926, 17606911.
29. Holton T, Hudspeth A. The transduction channel of hair cells from the bull-frog characterized by noise analysis. J Physiol 1986, 375:195-227. 1182755, 2432221.
30. Martin P, Mehta A, Hudspeth A. Negative hair-bundle stiffness betrays a mechanism for mechanical amplification by the hair cell. Proc Natl Acad Sci USA 2000, 97(22):12026-12031. 10.1073/pnas.210389497, 17288, 11027302.
31. Jacobs R, Hudspeth A. Ultrastructural correlates of mechanoelectrical transduction in hair cells of the bullfrog's internal ear. Cold Spring Harb Symp Quant Biol 1990, 55:547-561. 10.1101/SQB.1990.055.01.053, 1983446.
32. Matsui J, Ryals B. Hair cell regeneration: an exciting phenomenon...but will restoring hearing and balance be possible?. J Rehabil Res Dev 2005, 42(4 Suppl 2):187-198.
33. Manley GA, van Dijk P. Otoacoustic Emissions in Amphibians, Lepidosaurs, and Archosaurs. Active Processes and Otoacoustic Emissions in Hearing, vol. 30 2007, 211-260. Springer, New York, Manley Geoffrey A.
34. Wever E. Middle ear muscles of the frog. Proc Natl Acad Sci USA 1979, 76(6):3031-3033. 10.1073/pnas.76.6.3031, 383746, 288086.
35. Bever M, Jean Y, Fekete D. Three-dimensional morphology of inner ear development in Xenopus laevis. Dev Dyn 2003, 227(3):422-430. 10.1002/dvdy.10316, 12815629.
36. Kil S, Collazo A. Origins of inner ear sensory organs revealed by fate map and time-lapse analyses. Dev Biol 2001, 233(2):365-379. 10.1006/dbio.2001.0211, 11336501.
37. Quick Q, Serrano E. Inner ear formation during the early larval development of Xenopus laevis. Dev Dyn 2005, 234(3):791-801. 10.1002/dvdy.20610, 2829094, 16217737.
38. Quick Q, Serrano E. Cell proliferation during the early compartmentalization of the Xenopus laevis inner ear. Int J Dev Biol 2007, 51(3):201-209. 10.1387/ijdb.062176qq, 17486540.
39. Polimeni M, Prigioni I, Russo G, Calzi D, Gioglio L. Plasma membrane Ca2+-ATPase isoforms in frog crista ampullaris: identification of PMCA1 and PMCA2 specific splice variants. Hear Res 2007, 228(1-2):11-21.
40. Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Eichler EE, Ornitz DM, Green ED, Program NCS. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evol Biol 2011, 11:23. 10.1186/1471-2148-11-23, 3038909, 21261979.
41. Ramirez-Gordillo D, Trujillo-Provencio C, Knight VB, Serrano EE. Optimization of gene delivery methods in Xenopus laevis kidney (A6) and Chinese hamster ovary (CHO) cell lines for heterologous expression of Xenopus inner ear genes. In Vitro Cell Dev Biol Anim 2011, 47(9):640-652. 10.1007/s11626-011-9451-2, 21959846.
42. Hildebrand MS, de Silva MG, Klockars T, Campbell CA, Smith RJH, Dahl HHM. Gene expression profiling analysis of the inner ear. Hear Res 2007, 225(1-2):1-10.
43. Hellsten U, Harland R, Gilchrist M, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam N, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. The genome of the Western clawed frog Xenopus tropicalis. Science 2010, 328(5978):633-636. 10.1126/science.1183670, 2994648, 20431018.
44. Nieuwkoop PDaF J. Normal table of Xenopus laevis (Daudin): A systematical and chronological survey of the development from the fertilized egg till the end of metamorphosis, 2nd edn 1967, North Holland Publishers.
45. Segerdell E, Bowes J, Pollet N, Vize P. An ontology for Xenopus anatomy and development. BMC Dev Biol 2008, 8:92. 10.1186/1471-213X-8-92, 2561031, 18817563.
46. Amaya E. Xenomics. Genome Res 2005, 15(12):1683-1691. 10.1101/gr.3801805, 16339366.
47. Chesneau A, Sachs LM, Chai N, Chen Y, Du Pasquier L, Loeber J, Pollet N, Reilly M, Weeks DL, Bronchain OJ. Transgenesis procedures in Xenopus. Biol Cell 2008, 100(9):503-521. 10.1042/BC20070148, 2967756, 18699776.
48. Sczyrba A, Beckstette M, Brivanlou A, Giegerich R, Altmann C. XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. BMC Genomics 2005, 6:123. 10.1186/1471-2164-6-123, 1261260, 16162280.
49. Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD. Xenbase: gene expression and improved integration. Nucleic Acids Res 2010, 38(Database issue):D607-612.
50. Altmann CR, Bell E, Sczyrba A, Pun J, Bekiranov S, Gaasterland T, Brivanlou AH. Microarray-based analysis of early development in Xenopus laevis. Dev Biol 2001, 236(1):64-75. 10.1006/dbio.2001.0298, 11456444.
51. Gohin M, Bobe J, Chesnel F. Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates. BMC Genomics 2010, 11:18. 10.1186/1471-2164-11-18, 2821372, 20059772.
52. Munoz-Sanjuan I, Bell E, Altmann CR, Vonica A, Brivanlou AH. Gene profiling during neural induction in Xenopus laevis: regulation of BMP signaling by post-transcriptional mechanisms and TAB3, a novel TAK1-binding protein. Development 2002, 129(23):5529-5540. 10.1242/dev.00097, 12403722.
53. Baldessari D, Shin Y, Krebs O, Konig R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C. Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 2005, 122(3):441-475. 10.1016/j.mod.2004.11.007, 15763214.
54. Grow M, Neff AW, Mescher AL, King MW. Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration. Dev Dyn 2006, 235(10):2667-2685. 10.1002/dvdy.20897, 16871633.
55. Powers T, Virk S, Serrano E. Strategies for enhanced annotation of a microarray probe set. Int J Bioinform Res Appl 2010, 6(2):163-178. 10.1504/IJBRA.2010.032119, 2955980, 20223738.
56. HGNC Home Page http://www.genenames.org/.
57. Serrano E, Trujillo-Provencio C, Sultemeier D, Bullock W, Quick Q. Identification of genes expressed in the Xenopus inner ear. Cell Mol Biol (Noisy-le-Grand) 2001, 47(7):1229-1239.
58. Dennis GJ, Sherman B, Hosack D, Yang J, Gao W, Lane H, Lempicki R. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
59. Huang DW, Sherman B, Lempicki R. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
60. Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007, 8(9):R183.
61. Affymetrix Products-GeneChip Xenopus laevis Genome Array http://www.affymetrix.com/estore/browse/products.jsp?navMode=34000&productId=131526&navAction=jump&aId=productsNav, Affymetrix.
62. Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22(7):789-794. 10.1093/bioinformatics/btk046, 16410320.
63. Wu Z, Irizarry R. Preprocessing of oligonucleotide array data. Nat Biotechnol 2004, 22(6):656-658. author reply 658.
64. Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J. RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol 2001, 2(11). SOFTWARE0002.
65. Gong P, Pirooznia M, Guan X, Perkins EJ. Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida. PLoS One 2010, 5(12):e14266. 10.1371/journal.pone.0014266, 2999564, 21170345.
66. Gabashvili IS, Sokolowski BH, Morton CC, Giersch AB. Ion channel gene expression in the inner ear. J Assoc Res Otolaryngol 2007, 8(3):305-328. 10.1007/s10162-007-0082-y, 2538437, 17541769.
67. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ, . NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Broad Institute Children's Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346, NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Broad Institute Children's Hospital Oakland Research Institute.
68. Díaz ME, Varela-Ramírez A, Serrano EE. Quantity, bundle types, and distribution of hair cells in the sacculus of Xenopus laevis during development. Hear Res 1995, 91(1-2):33-42.
69. López-Anaya V, López-Maldonado D, Serrano E. Development of the Xenopus laevis VIIIth cranial nerve: increase in number and area of axons of the saccular and papillar branches. J Morphol 1997, 234(3):263-276. 10.1002/(SICI)1097-4687(199712)234:3<263::AID-JMOR5>3.0.CO;2-A, 9373966.
70. Steel K, Bussoli T. Deafness genes: expressions of surprise. Trends Genet 1999, 15(6):207-211. 10.1016/S0168-9525(99)01753-9, 10354578.
71. Friedman LM, Dror AA, Avraham KB. Mouse models to study inner ear development and hereditary hearing loss. Int J Dev Biol 2007, 51(6-7):609-631.
72. Anagnostopoulos AV. A compendium of mouse knockouts with inner ear defects. Trends Genet 2002, 18(10):499.
73. Wangemann P. Supporting sensory transduction: cochlear fluid homeostasis and the endocochlear potential. J Physiol 2006, 576(Pt 1):11-21. 1995626, 16857713.
74. Delprat B, Schaer D, Roy S, Wang J, Puel J, Geering K. FXYD6 is a novel regulator of Na, K-ATPase expressed in the inner ear. J Biol Chem 2007, 282(10):7450-7456.
75. Alvarado D, Veile R, Speck J, Warchol M, Lovett M. Downstream targets of GATA3 in the vestibular sensory organs of the inner ear. Dev Dyn 2009, 238(12):3093-3102. 10.1002/dvdy.22149, 3086404, 19924793.
76. Ohyama T, Basch ML, Mishina Y, Lyons KM, Segil N, Groves AK. BMP signaling is necessary for patterning the sensory and nonsensory regions of the developing mammalian cochlea. J Neurosci 2010, 30(45):15044-15051. 10.1523/JNEUROSCI.3547-10.2010, 3074492, 21068310.
77. Thalmann I, Kohut R, Ryu J, Comegys T, Senarita M, Thalmann R. Protein profile of human perilymph: in search of markers for the diagnosis of perilymph fistula and other inner ear disease. Otolaryngol Head Neck Surg 1994, 111(3 Pt 1):273-280.
78. The National Xenopus Resource at the Marine Biological Laboratory http://mblwhoilibrary.mbl.edu/xenopus/index.html.
79. Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E. RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20. 10.1007/978-1-59745-523-7_1, 18839338.
80. Wu Z. A review of statistical methods for preprocessing oligonucleotide microarrays. Stat Methods Med Res 2009, 18(6):533-541. 10.1177/0962280209351924, 3152825, 20048383.
81. Wu Z, Irizarry R, Gentlemen R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004, 99(468):909-917.
82. Bioconductor Task View: Software http://www.bioconductor.org/packages/release/Software.html.
83. The Comprehensive R Archive Network http://cran.cnr.berkeley.edu/.
84. Affymetrix GeneChip Expression Analysis: Data Analysis Fundamentals. In Manual 2004, Affymetrix.
85. Hereditary Hearing Loss [http://hereditaryhearingloss.org].
86. Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
87. OMIM http://www.ncbi.nlm.nih.gov/omim/.
88. Consortium U The Universal Protein Resource (UniProt). Nucleic Acids Res 2007, 35(Database issue):D193-197. Consortium U.
89. The Ion Channel Database [http://www.ionchannels.org/database.php].
90. IUPHAR Database of Receptors and Ion Channels http://www.iuphar-db.org/index.jsp.
91. Affymetrix-NetAffx Analysis Center https://www.affymetrix.com/analysis/index.affx.
92. Ensembl Genome Browser [http://uswest.ensembl.org/index.html].
93. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
94. JGI Xenopus tropicalis v4.1 http://genome.jgi-psf.org/Xentr4/Xentr4.home.html.
95. Xenopus tropicalis v4.1 - Download http://genome.jgi-psf.org/Xentr4/Xentr4.download.ftp.html.
96. Sambrook J, Russell DW. Molecular cloning : a laboratory manual 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 3.