A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Espinosa, Octavio ^a,b,c   Hancock, John M ^a  

^a MRC MAMMALIAN GENETICS UNIT   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE EXPRESSION; GENETIC ASSOCIATION; GENOTYPE PHENOTYPE CORRELATION; NONHUMAN; PHENOTYPE; PLEIOTROPY; PROTEIN PROTEIN INTERACTION; ANIMAL; BIOLOGY; GENE; GENE REGULATORY NETWORK; GENETIC DATABASE; HUMAN; MOLECULAR GENETICS; MOUSE; PHYLOGENY; PHYSIOLOGY;

MAMMALIA;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE REGULATORY NETWORKS; GENES; GENETIC ASSOCIATION STUDIES; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; PHYLOGENY;

EID: 79956275109     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019693     Document Type: Article

References (44)

1. Brown SD, Wurst W, Kuhn R, Hancock J, (2009) The Functional Annotation of Mammalian Genomes: The Challenge of Phenotyping. Annu Rev Genet 43: 305-333.
2. Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT, (2010) The Mouse Genome Database: enhancements and updates. Nucleic Acids Res 38: D586-592.
3. Hancock JM, Mallon A-M, (2007) Phenobabelomics-mouse phenotype data resources. Brief Funct Genomic Proteomic 6: 292-301.
4. Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM, (2010) Phenotype ontologies for mouse and man; bridging the semantic gap. Disease Models & Mechanisms 3: 281-289.
5. Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, et al. (2009) Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome 20: 457-461.
6. Smith CL, Goldsmith CA, Eppig JT, (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6: R7.
7. Morgan H, Beck T, Blake A, Gates H, Adams N, et al. (2010) EuroPhenome: a repository for high-throughput mouse phenotyping data. Nucleic Acids Res 38: D577-585.
8. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
9. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
10. Butte AJ, Kohane IS, (2006) Creation and implications of a phenome-genome network. Nat Biotechnol 24: 55-62.
11. Jiang JQ, Dress AW, Chen M, (2010) Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network. J Integr Bioinform 7 doi:10.2390/biecoll-jib-2010-2149.
12. Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C, (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol 10: R91.
13. Wu X, Jiang R, Zhang MQ, Li S, (2008) Network-based global inference of human disease genes. Mol Syst Biol 4: 189.
14. Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY, (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 28: 149-156.
15. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, et al. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181-188.
16. McGary KL, Lee I, Marcotte EM, (2007) Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol 8: R258.
17. Kim WK, Krumpelman C, Marcotte EM, (2008) Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol 9 (Suppl 1): S5.
18. Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, et al. (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 9 (Suppl 1): S2.
19. Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, et al. (2008) Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol 9 (Suppl 1): S3.
20. Groth P, Weiss B, Pohlenz HD, Leser U, (2008) Mining phenotypes for gene function prediction. BMC Bioinformatics 9: 136.
21. Newman ME, (2006) Modularity and community structure in networks. Proc Natl Acad Sci U S A 103: 8577-8582.
22. Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
23. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
24. Vinogradov AE, (2010) Systemic factors dominate mammal protein evolution. Proc R Soc B 277: 1403-1408.
25. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327-335.
26. Schaefer E, Durand M, Stoetzel C, Doray B, Viville B, et al. (2010) Molecular diagnosis reveals genetic heterogeneity for the overlapping MKKS and BBS phenotypes. Eur J Med Genet.
27. Shimodaira H, (2008) Testing Regions with Nonsmooth Boundaries via Multiscale Bootstrap. Journal of Statistical Planning and Inference 138: 1227-1241.
28. Beck T, Morgan H, Blake A, Wells S, Hancock JM, et al. (2009) Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics 10 (Suppl 5): S2.
29. Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M, (2004) Genomic analysis of essentiality within protein networks. Trends Genet 20: 227-231.
30. Jeong H, Mason SP, Barabasi AL, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
31. McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, et al. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A 107: 6544-6549.
32. Houle D, Govindaraju DR, Omholt S, (2010) Phenomics: the next challenge. Nat Rev Genet 11: 855-866.
33. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, et al. (2005) Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436: 861-865.
34. Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, et al. (2010) Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol 6: 370.
35. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
36. Strimmer K, (2008) fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24: 1461-1462.
37. Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, et al. (2004) The functional landscape of mouse gene expression. J Biol 3: 21.
38. Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, et al. (2010) The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 38 doi:10.1093/nar/gkq1132 [Epub ahead of print].
39. Ringwald M, Eppig JT, Kadin JA, Richardson JE, (2000) GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements. The Gene Expression Database group. Nucleic Acids Res 28: 115-119.
40. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35: D561-565.
41. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-539.
42. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21: 832-834.
43. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-451.
44. Suzuki R, Shimodaira H, (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22: 1540-1542.