Phenosite: A web database integrating the mouse phenotyping platform and the experimental procedures in mice

Journal of Bioinformatics and Computational Biology

Volumn 5, Issue 6, 2007, Pages 1173-1191

  Masuya, Hiroshi ^a   Yoshikawa, Sumi ^a   Heida, Naohiko ^a   Toyoda, Tetsuro ^a   Wakana, Shigeharu ^a   Shiroishi, Toshihiko ^a  

^a RIKEN   (Japan)

Author keywords

Baseline data; Database; Integration; Mouse; Ontology; Phenotype; Protocol; Terminology

Indexed keywords

ETHYLNITROSOUREA; GENOMIC DNA;

ACCESS TO INFORMATION; ANIMAL GENETICS; ANIMAL MODEL; ARTICLE; BIOLOGY; FEMALE; GENE LIBRARY; GENE MAPPING; GENETIC ANALYSIS; GENETIC CODE; GENETIC DATABASE; INDUCED MUTATION; INFORMATION STORAGE; MALE; MOUSE; MUTAGENESIS; NOMENCLATURE; NONHUMAN; PHENOME SEMANTICS INFORMATION WITH TERMINOLOGY OF EXPERIMENT; PHENOTYPE; PHENOTYPIC VARIATION;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; INTERNET; MALE; MICE; MICE, INBRED C57BL; MICE, INBRED DBA; MODELS, ANIMAL; MUTAGENESIS; MUTATION; PHENOTYPE;

MUS;

EID: 37849003472     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720007003168     Document Type: Article

References (34)

1. Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT, Grieder FB, Heintz N, Hicks G, Insel TR, Joyner A, Koller BH, Lloyd KC, Magnuson T, Moore MW, Nagy A, Pollock JD, Roses AD, Sands AT, Seed B, Skarnes WC, Snoddy J, Soriano P, Stewart DJ, Stewart F, Stillman B, Varmus H, Varticovski L, Verma IM, Vogt TF, von Melchner H, Witkowski J, Woychik RP, Wurst W, Yancopoulos GD, Young SG, Zambrowicz B, The knockout mouse project, Nat Genet 36 (9):921-924, 2004.
2. Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmelict P, Chambon P, Cox R, Davidson D, Davies K, Duboule D, Forejt J, Granucci F, Hastie N, de Angelis MH, Jackson I, Kioussis D, Kollias G, Lathrop M, Lendahl U, Malumbres M, von Melchner H, Muller W, Partanen J, Ricciardi-Castagnoli P, Rigby P, Rosen B, Rosenthal N, Skarnes B, Stewart AF, Thornton J, Tocehini-Valentini G, Wagner E, Wahli W, Wurst W, The European dimension for the mouse genome mutagenesis program, Nat Genet 36(9):925-927, 2004.
3. Grimm D, NIH knocks out key mouse house, Science 312 5782):1863, 2006.
4. Collins FS, Rossant J, Wurst W, International Mouse Knockout Consortium: A mouse for all reasons, Cell 128(1):9-13, 2007.
5. Hitotsumachi S, Carpenter DA, Russell WL, Dose-repetition increases the mutagenic effectiveness of N-ethyl-N-nitrosourea in mouse spermatogonia, Proc Natl Acad Sci USA 82(19):6619-6621, 1985.
6. Russell LB, Bangham JW, Stelzner KF, Hunsicker PR, High frequency of mosaic mutants produced by N-ethyl-N-nitrosourea exposure of mouse zygotes, Proc Natl Acad Sci USA 85(23):9167-9170, 1988.
7. Rinchik EM, Carpenter DA, N-ethyl-N-nitrosourea mutagenesis of a 6- to 11-cM subregion of the Fah-Hbb interval of mouse chromosome 7: Completed testing of 4557 gametes and deletion mapping and complementation analysis of 31 mutations, Genetics 152(1):373-383, 1999.
8. Nolan PM, Peters J, Strivens M, Rogers D, Hagan J, Spurr N, Gray IC, Vizor L, Brooker D, Whitehill E, Washbourne R, Hough T, Greenaway S, Hewitt M. Liu X, McCormack S, Pickford K, Selley R, Wells C, Tymowska-Lalanne Z, Roby P, Glenister P, Thornton C, Thaung C, Stevenson JA, Arkell R, Mburu P, Hardisty R, Kienan A, Erven A, Steel KP, Voegeling S, Guenet JL, Nickols C, Sadri R, Nasse M, Isaacs A, Davies K, Browne M, Fisher EM, Martin J, Rastan S, Brown SD, Hunter J, A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse, Nat Genet 25(4):440-443, 2000.
9. Hrabe de Angelis MH, Flaswinkel H, Fuchs H, Rafhkolb B, Soewarto D, Marschall S, Heffner S, Pargent W, Wuensch K, Jung M, Reis A, Richter T, Alessandrini F, Jakob T, Fuchs E, Kolb H, Kremmer E, Schaeble K, Rollinski B, Roscher A, Peters C, Meitinger T, Strom T, Steckler T, Holsboer F, Klopstock T, Gekeler F, Schindewolf C, Jung T, Avraham K, Behrendt H, Ring J, Zimmer A, Schughart K, Pfeffer K, Wolf E, Balling R, Genome-wide, large-scale production of mutant mice by ENU mutagenesis, Nat Genet 25(4):444-447, 2000.
10. Kile BT, Hentges KE, Clark AT, Nakamura H, Salinger AP, Liu B, Box N, Stockton DW, Johnson RL, Behringer RR, Bradley A, Justice MJ, Functional genetic analysis of mouse chromosome 11, Nature 425 (6953):81-86, 2003.
11. Masuya H, Nakai Y, Motegi H, Niinaya N, Kida Y, Kancko Y, Aritake H, Suzuki N, Ishii J, Koorikawa K, Suzuki T, Inoue M, Kobayashi K, Toki H, Wada Y, Kaneda H, Ishijima J, Takahashi KR, Minowa O, Noda T, Wakana S, Gondo Y, Shiroishi T, Development arid implementation of a database system to manage a large-scale mouse ENU-mutagenesis program, Mamm Genome 15(5):404-411, 2004.
12. Goldowitz D, Frankel WN, Takahashi JS, Holtz-Vitaterna M, Bult C, Kibbe WA, Snoddy J, Li Y, Pretel S, Yates J, Swanson DJ, Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function, Mol Brain Res 132 (2): 105-115, 2004.
13. Wilson L, Ching YH, Farias M, Hartford SA, Howell G, Shao H, Bucan M, Schimenti JC, Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations, Genonte Res 15 (8):1095-1105, 2005.
14. Masuya H, Inoue M, Wada Y, Shimizu A, Nagano J, Kawai A, Inoue A, Kagami T, Hirayarna T, Yamaga A, Kaneda H, Kobayashi K, Minowa O, Miura I, Gondo Y, Noda T, Wakana S, Shiroishi T, Implementation of the modified-SHIRPA protocol for screening of dominant phenotypes in a large-scale ENU mutagenesis program, Mamm Genome 16 (11):829-837, 2005.
15. Vivian JL, Chen Y, Yee D, Schneider E, Magnuson T, An allelic series of mutations in Smad2 and Smad4 identified in a genotype-based screen of N-ethyl-N-nitrosourea-mutagenized mouse embryonic stem cells, Proc Natl Acad Sci USA 99(24):15542-15547, 2002.
16. Inoue M, Sakuraba Y, Motegi H, Kubota N, Toki H, Matsui J, Toyoda Y, Miwa I, Terauchi Y, Kadowaki T, Shigeyama Y, Kasuga M, Adachi T, Fujimoto N, Matsumoto R, Tsuchihashi K, Kagami T, Inoue A, Kaneda H, Ishijima J, Masuya H, Suzuki T, Wakana S, Gondo Y, Minowa O, Shiroishi T, Noda T, A series of maturity onset diabetes of the young, type 2 (MODY2) mouse models generated by a large-scale ENU Mutagenesis program, Hum Mol Genet 13(11):1147-1157, 2004.
17. Quwailid MM, Hugill A, Dear N, Vizor L, Wells S, Horner E, Fuller S, Weedon J, McMath H, Woodman P, Edwards D, Campbell D, Rodger S, Carey J, Roberts A, Glenister P, Lalanne Z, Parkinson N, Coghill EL, McKeone R, Cox S, Willan J, Greenfield A, Keays D, Brady S, Spurr N, Cray I, Hunter J, Brown SD, Cox RD, A gene-driven ENU-based approach to generating an allelic series in any gene, Mamm Genome 15(8):585-591, 2004.
18. Masuya H, Shimizu K, Sezutsu H, Sakurata Y, Nagano J, Shimizu A, Fujimoto N, Kawai A, Miura I, Kaneda H, Kobayashi K, Ishijima J, Maeda T, Gondo Y, Noda T, Wakana S, Shiroishi T, Enamelin (Enam) is essential for amelogenesis: ENU-induced mouse mutants as models for different clinical subtypes of human amelogenesis imperfecta (AI), Hum Mol Genet 14(5):575-583, 2005.
19. Graw J, Loster J, Puk O, Munster D, Haubst N, Soewarto D, Fuchs H, Meyer B, Nurnberg P, Protsch W, Selby P, Favor J, Wolf E, Hrabe de Angelis M, Three novel Pax6 alleles in the mouse leading to the same small-eye phenotype caused by different consequences at target promoters, Invest Ophthalmol Vis Sci 46(12):4671-4683, 2005.
20. Strivens MA, Selley RL, Greenaway SJ, Hewitt M, Liu X, Battershill K, McCormack SL, Pickford KA, Vizor L, Nolan PM, Hunter AJ, Peters J, Brown SD, Informatics for mutagenesis: The design of Mutabase - A distributed data recording system for animal husbandry, mutagenesis, and phenotypic analysis, Mamm Genome 11(7):577-583, 2000.
21. Pagent W, Heffner S, Schäble FS, Soewarto D, Fuchs H, Angelis MH, MouseNet ©database: Digital management of a large-scale mutagenesis project, Mamm Genomic 11(7):590-593, 2000.
22. Brown SDM, Chambon P, Hrabe de Angelis M, Eumorphia Consortium, EMPReSS: Standardized phenotype screens for functional annotation of the mouse genome, Nat Genet 37(11):1155, 2005.
23. Green EC, Gkoutos GV, Lad HV, Blake A, Weekes J, Hancock JM, EMPReSS: European Mouse Phenotyping Resource for Standardized Screens, Bioinformatics 21(12):2930-2931, 2005.
24. Bodenreider O, Stevens R, Bio-ontologies: Current trends and future directions, Brief Bioinform 7(3):256-274, 2006.
25. Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, The Mouse Genome Database (MGD): From genes to mice - A community resource for Mouse biology, Nucleic Acids Res 33(Database issue):D471-D475, 2005.
26. Blake JA, Eppig JT, Bult CJ, Kadin JA, Richardson JE, The Mouse Genome Database (MGD): Updates and enhancements, Nucleic Acids Res 34 Database issue): D562-D567, 2006.
27. Smith CL, Goldsmith CA, Eppig JT, The Mammalian Phenotype Ontology as a tool for aunotating, analyzing and comparing phenotypic information, Genome Biol 6(1):R7, 2005.
28. The Mouse Phenotype Database Integration Consortium, Integration of mouse phenome data. resources, Mamm Genome 18(3):157-163, 2007.
29. Brown SD, Hancock JM, Gates H, Understanding mammalian genetic systems: The challenge of phenotyping in the mouse, PLoS Genet 2 (8):e118, 2006.
30. Cassman M, Barriers to progress M systems biology, Nature 438 7071):1079, 2005.
31. Gkoutos GV, Green ECJ, Mallon AM, Hancock JM, Davidson D, Using ontologies to describe mouse phenotypes, Genome Biol 6 (1):R8, 2005.
32. Wahlsten D, Metten P, Phillips TJ, Boehm SL 2nd, Burkhart-Kasch S, Dorow J, Doerksen S, Downing C, Fogarty J, Rodd-Henricks K. Hen R, McKinnon CS, Merrill CM, Nolte C, Schalomon M, Schlumbohm JP, Sibert JR, Wenger CD, Dudek BC, Crabbe JC, Different data from different labs: Lessons from studies of gene-environment interaction, J Neurobiol 54 (1):283-311, 2003.
33. Tucci V, Lad HV, Parker A, Polley S, Brown SD, Nolan PM, Gene-environment interactions differentially affect mouse strain behavioral parameters, Mamm Genome 17(11):1113-1120, 2006.
34. Yoshikawa S, Satou K, Konagaya A, Drug Interaction Ontology (DIO) for inferences of possible drug drug interactions, Medinfo 11(Pt 1):415-458, 2004.