RESUMO
The structured description of mutant phenotypes presents a major conceptual and practical problem. A general model for generating mouse phenotype ontologies that involves combing a variety of different ontologies to better link and describe phenotypes is presented. This model is based on the Phenotype and Trait Ontology schema proposal and incorporates practical limitations and designing solutions in an attempt to model a testbed for the first phenotype ontology constructed in this manner, namely the mouse behavior phenotype ontology. We propose the application of such a model could provide curators with a powerful mechanism of annotation, mining and knowledge representation as well as achieving some level of free text disassociation.
Assuntos
Biologia Computacional , Fenótipo , Animais , Simulação por Computador , Genômica/estatística & dados numéricos , Camundongos , Modelos Genéticos , Mutação , SoftwareRESUMO
Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologies. We also describe tools for storing, browsing and searching such complex ontologies. Central to this approach is that assays (protocols for measuring phenotypic characters) describe what has been measured as well as how this was done, allowing assays to link individual organisms to ontologies describing phenotypes. We have evaluated this approach by automatically annotating data on 600,000 mutant mice phenotypes using the SHIRPA protocol. We believe this approach will enable the flexible, extensible and detailed description of phenotypes from any organism.
RESUMO
Having a working draft of the human genome sequence is proving invaluable to mouse genetic and genomic studies, providing a useful stepping-stone towards the finished sequence of the mouse genome.
Assuntos
Sequência Conservada , Evolução Molecular , Genoma Humano , Camundongos/genética , Animais , Humanos , Análise de Sequência de DNARESUMO
The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions.
Assuntos
Proteínas Cromossômicas não Histona , Análise de Sequência de DNA , Cromossomo X/genética , 3-Hidroxiesteroide Desidrogenases/genética , Sequência de Aminoácidos , Animais , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/isolamento & purificação , Proteínas de Ligação ao Cálcio/genética , Proteínas do Citoesqueleto , Proteínas de Ligação a DNA/genética , Biblioteca Genômica , Humanos , Proteínas com Domínio LIM , Antígenos Específicos de Melanoma , Camundongos , Dados de Sequência Molecular , Família Multigênica , Proteínas de Neoplasias/genética , Proteínas Nucleares/genética , Homologia de Sequência do Ácido Nucleico , Dedos de Zinco/genéticaRESUMO
X-linked dominant disorders that are exclusively lethal prenatally in hemizygous males have been described in human and mouse. None of the genes responsible has been isolated in either species. The bare patches (Bpa) and striated (Str) mouse mutations were originally identified in female offspring of X-irradiated males. Subsequently, additional independent alleles were described. We have previously mapped these X-linked dominant, male-lethal mutations to an overlapping region of 600 kb that is homologous to human Xq28 (ref. 4) and identified several candidate genes in this interval. Here we report mutations in one of these genes, Nsdhl, encoding an NAD(P)H steroid dehydrogenase-like protein, in two independent Bpa and three independent Str alleles. Quantitative analysis of sterols from tissues of affected Bpa mice support a role for Nsdhl in cholesterol biosynthesis. Our results demonstrate that Bpa and Str are allelic mutations and identify the first mammalian locus associated with an X-linked dominant, male-lethal phenotype. They also expand the spectrum of phenotypes associated with abnormalities of cholesterol metabolism.
