Mousefinder: Candidate disease genes from mouse phenotype data

Human Mutation

Volumn 33, Issue 5, 2012, Pages 858-866

  Chen, Chao Kung ^a   Mungall, Christopher J ^b   Gkoutos, Georgios V ^c   Doelken, Sandra C ^d,e   Kohler, Sebastian ^d   Ruef, Barbara J ^f   Smith, Cynthia ^g   Westerfield, Monte ^f   Robinson, Peter N ^d,e   Lewis, Suzanna E ^b   Schofield, Paul N ^c,g   Smedley, Damian ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^e MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^f UNIVERSITY OF OREGON   (United States)

^g JACKSON LABORATORY   (United States)

Author keywords

Candidate disease genes; Model organism; Mouse; Phenotype

Indexed keywords

ARTICLE; ARTN GENE; CHROMOSOME 1P; COMPUTER PROGRAM; DATA MINING; DISEASE MODEL; GENE; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC DISORDER; HUMAN; INTERNET; MOUSE; NONHUMAN; ORTHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PTOSIS; SEMANTICS; ANIMAL; DISEASES; GENETIC ASSOCIATION; GENETIC DATABASE; GENETICS; MOLECULAR GENETICS; MUTATION; NOMENCLATURE; ONLINE SYSTEM;

ANIMALS; DATABASES, GENETIC; DISEASE; DISEASE MODELS, ANIMAL; GENETIC ASSOCIATION STUDIES; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; MUTATION; ONLINE SYSTEMS; PHENOTYPE; TERMINOLOGY AS TOPIC;

EID: 84864349644     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22051     Document Type: Article

References (23)

1. Abbott A. 2010. Mouse megascience. Nature 465:526.
2. Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT; Mouse Genome Database Group. 2011. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res 39:D842-D848.
3. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN. 2009. Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc 2009: 7069-7072
4. Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz H-D, Weiss B. 2006. Phenomic DB: a new cross-species genotype/phenotype resource. Nucleic Acids Res 35:D696-D699.
5. Hoehndorf, R Schofield PN, Gkoutos GV. 2011. Phenome NET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res 39:e119.
6. Honma Y, Araki T, Gianino S, Bruce A, Heuckeroth R, Johnson E, Milbrandt J. 2002. Artemin is a vascular-derived neurotropic factor for developing sympathetic neurons. Neuron 35:267-282.
7. Kitsios GD, Tangri N, Castaldi PJ, Ioannidis JP. 2010. Laboratory mouse models for the human genome-wide associations. PLo S One 5:e13782.
8. Köhler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN. 2011. Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics 12:418.
9. Meehan TF, Carr CJ, Jay JJ, Bult CJ, Chesler EJ, Blake JA. 2011. Autism candidate genes via mouse phenomics. J Biomed Inform. 44:S5-S11.
10. Mungall C., Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M. 2010. Integrating phenotype ontologies across multiple species. Genome Biol 11: R2.
11. Quartu M, Serra MP, Boi M, Sestu N, Lai ML, Del Fiacco M. 2007. Tissue distribution of neurturin, persephin and artemin in the human brainstem at fetal, neonatal and adult age. Brain Res 1143:102-115.
12. Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC. 2011. Nucleic Acids Res 39:D842-D848.
13. Robinson PN, Koehler S, Bauer S, Seelow D, Horn D, Mundlos S. 2008. The human phenotype ontology: a tool for annotating and analyzinghumanhereditary disease. Am J Hum Genet 83:610-615.
14. Rosenthal N, Brown S. 2007. The mouse ascending: perspectives for human-disease models. Nat Cell Biol 9:993-999.
15. Sardana D, Vasa S, Vepachedu N, Chen J, Gudivada RC, Aronow BJ, Jegga AG. 2010. Pheno HM: human-mouse comparative phenome-genome server. Nucleic Acids Res 38:W165-W174.
16. Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM. 2010. Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech 3: 281-289.
17. Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A. 2011. Aconditional knockout resource for the genome-wide study of mouse gene function. Nature 474:337-342.
18. Smith CL, Eppig JT. 2009. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med 1:390-399.
19. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M. 2008. The zebrafish information network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 36:D768-D772.
20. Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H. 2011. Anatomy ontologies and potential users: bridging the gap. J Biomed Semantics 2(S4):S3.
21. Tweedie S, Ashburner M, Falls K, Leyland P, Mc Quilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H; Fly Base Consortium. 2009. Fly Base: enhancing Drosophila gene ontology annotations. Nucleic Acids Res 37:D555-D559.
22. Twigger, SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team. 2007. The Rat Genome Database, update 2007-easing the path from disease to data and back again. Nucleic Acids Res 35:D658-D662.
23. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. 2009. Linking human diseases to animal models using ontology-based phenotype annotation. PLo S Biol 7: e1000247.