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Janan T Eppig

Publications and source records attributed to Janan T Eppig.

At least 19 recordsLinked to original sources
PubMed2006

The mouse genome database (MGD): new features facilitating a model system.

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

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PubMed2006

Mouse Tumor Biology Database (MTB): status update and future directions.

The Mouse Tumor Biology (MTB) database provides access to data about endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant and genetically engineered mice). Data include information on the frequency and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background and literature or contributor citations. Data are curated from the primary literature or submitted directly from researchers. MTB is accessed via the Mouse Genome Informatics web site (http://www.informatics.jax.org). Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature, when available. Recently MTB has been redesigned and its database infrastructure replaced with a robust relational database management system (RDMS). Web interface improvements include a new advanced query form and enhancements to already existing search capabilities. The Tumor Frequency Grid has been revised to enhance interactivity, providing an overview of reported tumor incidence across mouse strains and an entrée into the database. A new pathology data submission tool allows users to submit, edit and release data to the MTB system.

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PubMed2006

The mouse Gene Expression Database (GXD): 2007 update.

The Gene Expression Database (GXD) provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, GXD aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of GXD has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and cDNA screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. GXD is available through the MGI web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtml.

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PubMed2006

The Mouse Genome Database (MGD): updates and enhancements.

The Mouse Genome Database (MGD) integrates genetic and genomic data for the mouse in order to facilitate the use of the mouse as a model system for understanding human biology and disease processes. A core component of the MGD effort is the acquisition and integration of genomic, genetic, functional and phenotypic information about mouse genes and gene products. MGD works within the broader bioinformatics community to define referential and semantic standards to facilitate data exchange between resources including the incorporation of information from the biomedical literature. MGD is also a platform for computational assessment of integrated biological data with the goal of identifying candidate genes associated with complex phenotypes. MGD is web accessible at http://www.informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources.

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PubMed2005

The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

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PubMed2005

High incidence, early onset of histiocytic sarcomas in mice with Hertwig's anemia.

OBJECTIVE: Histiocytic sarcoma (HS) is a rare, rapidly disseminated, usually lethal tumor in humans. Treatment specific for HS has not been developed primarily due to deficiencies of appropriate animal models with high incidence/early onset. Mice with Hertwig's anemia (an/an) provide a potential model. METHODS: Here, we compare HS susceptibility in an/an and unaffected control mice maintained on three genetic backgrounds. As a potential therapeutic measure, genetically marked bone marrow is transplanted between high and low susceptibility animals. RESULTS: HS is detected earlier and the overall incidence is 15-fold higher in WBB6F1(F1)-an/an than in F1-+/?, B6-an/an and -+/? mice. Neither WB-an/an nor their normal WB-+/? littermates present with HS. Liver myelopoiesis and aneuploidy coexist with HS but the former is also rampant (33.7% incidence) in HS-free +/? and an/an mice. Marrow transplantation experiments provide evidence that (1) myelopoiesis is associated with HS and (2) early-onset/high-incidence HS is blocked by using late-onset F1-+/+ mice, as either donor or recipient. CONCLUSIONS: Homozygosity for an on an F1 genetic background is essential for high-incidence/early-onset HS; myelopoiesis and HS coexist; and therapeutic transplantation may be feasible.

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PubMed2004

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease. The MP Ontology supports different levels and richness of phenotypic knowledge and flexible annotations to individual genotypes. It continues to develop dynamically via collaborative input from research groups, mutagenesis consortia, and biological domain experts. The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data.

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PubMed2004

Proteotypic classification of spontaneous and transgenic mammary neoplasms.

INTRODUCTION: Mammary tumors in mice are categorized by using morphologic and architectural criteria. Immunolabeling for terminal differentiation markers was compared among a variety of mouse mammary neoplasms because expression of terminal differentiation markers, and especially of keratins, provides important information on the origin of neoplastic cells and their degree of differentiation. METHODS: Expression patterns for terminal differentiation markers were used to characterize tumor types and to study tumor progression in transgenic mouse models of mammary neoplasia (mice overexpressing Neu (Erbb2), Hras, Myc, Notch4, SV40-TAg, Tgfa, and Wnt1), in spontaneous mammary carcinomas, and in mammary neoplasms associated with infection by the mouse mammary tumor virus (MMTV). RESULTS: On the basis of the expression of terminal differentiation markers, three types of neoplasm were identified: first, simple carcinomas composed exclusively of cells with a luminal phenotype are characteristic of neoplasms arising in mice transgenic for Neu, Hras, Myc, Notch4, and SV40-TAg; second, 'complex carcinomas' displaying luminal and myoepithelial differentiation are characteristic of type P tumors arising in mice transgenic for Wnt1, neoplasms arising in mice infected by the MMTV, and spontaneous adenosquamous carcinomas; and third, 'carcinomas with epithelial to mesenchymal transition (EMT)' are a characteristic feature of tumor progression in Hras-, Myc-, and SV40-TAg-induced mammary neoplasms and PL/J and SJL/J mouse strains, and display de novo expression of myoepithelial and mesenchymal cell markers. In sharp contrast, EMT was not detected in papillary adenocarcinomas arising in BALB/cJ mice, spontaneous adenoacanthomas, neoplasms associated with MMTV-infection, or in neoplasms arising in mice transgenic for Neu and Wnt1. CONCLUSIONS: Immunohistochemical profiles of complex neoplasms are consistent with a stem cell origin, whereas simple carcinomas might originate from a cell committed to the luminal lineage. In addition, these results suggest that the initiating oncogenic events determine the morphologic features associated with cancer progression because EMT is observed only in certain types of neoplasm.

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PubMed2004

The mouse Gene Expression Database (GXD): updates and enhancements.

The Gene Expression Database (GXD) is a community resource for gene expression information in the laboratory mouse. By collecting and integrating different types of expression data, GXD provides information about expression profiles in different mouse strains and mutants. Participation in the Gene Ontology (GO) project classifies genes and gene products with regard to molecular functions, biological processes, and cellular components. Integration with other Mouse Genome Informatics (MGI) databases places the gene expression information in the context of mouse genetic, genomic and phenotypic information. The integration of these types of information enables valuable insights into the molecular biology that underlies development and disease. The utility of GXD has been improved by the daily addition of new data and through the implementation of new query and display features. These improvements make it easier for users to interrogate and visualize expression data in the context of their specific needs. GXD is accessible through the MGI website at http://www.informatics.jax.org/ or directly at http://www. informatics.jax.org/menus/expression_menu.shtml.

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PubMed2004

The Mouse Genome Database (MGD): integrating biology with the genome.

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

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PubMed2004

Visualizing the laboratory mouse: capturing phenotype information.

A concerted effort to develop myriad new phenotypic alleles through mutagenesis programs presents new challenges for the biomedical community and for the informatics infrastructure needed to support this work. To handle and co-ordinate large programs of treatment, breeding, and sequential or longitudinal testing for a variety of obvious and subtle traits requires sophisticated data management software. Further, trait analyses, heritability testing, and animal availability and status must be captured and disseminated to the wider community. The Mouse Genome Database (MGD) will serve as the central integration point for the various mutagenesis programs, registering new alleles, providing accession identifiers, and capturing phenotypic descriptions. In addition, MGD will provide public access to unified searches over all alleles with links to the centres of origin for detailed testing data.

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PubMed2004

The knockout mouse project.

Mouse knockout technology provides a powerful means of elucidating gene function in vivo, and a publicly available genome-wide collection of mouse knockouts would be significantly enabling for biomedical discovery. To date, published knockouts exist for only about 10% of mouse genes. Furthermore, many of these are limited in utility because they have not been made or phenotyped in standardized ways, and many are not freely available to researchers. It is time to harness new technologies and efficiencies of production to mount a high-throughput international effort to produce and phenotype knockouts for all mouse genes, and place these resources into the public domain.

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PubMed2003

MGD: the Mouse Genome Database.

The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental details annotated from both literature and on-line genomic data sources. MGD curates and presents the consensus representation of genotype (sequence) to phenotype information including highly detailed information about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse. Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system.

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PubMed2003

The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies.

We have developed a unique comprehensive mouse radiation hybrid (RH) map of nearly 23,000 markers integrating data from three international genome centers and over 400 independent laboratories. We have cross-referenced this map to the 0.5-cM resolution recombination-based Jackson Laboratory (TJL) backcross panel map, building a complete set of RH framework chromosome maps based on a high density of known-ordered anchor markers. We have systematically typed markers to improve coverage and resolve discrepancies, and have reanalyzed data sets as needed. The cross-linking of the RH and recombination maps has resulted in a highly accurate genome-wide map with consistent marker order. We have compared these linked framework maps to the Ensemble mouse genome sequence assembly, and show that they are a useful medium resolution tool for both validating sequence assembly and elucidating chromosome biology.

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PubMed2003

Connecting sequence and biology in the laboratory mouse.

The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.

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PubMed2002

The Mouse Tumor Biology Database: a public resource for cancer genetics and pathology of the mouse.

Developing genetic mouse models for cancer research has been recognized as an "exceptional opportunity" by the National Cancer Institute. The establishment of bioinformatics resources to facilitate access to published and unpublished data on the genetics and pathology of cancer in different strains of the laboratory mouse is critical to developing and using mouse models of human disease. In this article, we review the Mouse Tumor Biology Database (MTB), a public resource for information on cancer genetics, epidemiology, and pathology in genetically defined mice. We outline current content, data acquisition strategies, and query mechanisms for MTB. MTB is accessible on-line at http://tumor.informatics.jax.org.

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PubMed2002

The Mouse Genome Database (MGD): the model organism database for the laboratory mouse.

The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD strives to provide a highly curated, highly integrated information resource that not only includes the consensus view of current knowledge about the mouse, but also provides comparative genomic information particularly for human and rat genomes. MGD includes extensive information about mouse genes, supporting all gene attribute assertions with experimental data, statements of evidence and citation. Detailed information about alleles and mouse mutants includes genotype, molecular variant and phenotype descriptions. Extensive collaboration with other data providers such as NCBI, RIKEN and SWISS-PROT provides standardization of gene:sequence associations and robust interconnections between large information systems based on shared sequence curation. Recent integration of large datasets of mouse full-length cDNAs and radiation-hybrid mapped ESTs, the continued development and use of extensive structured vocabularies and the expansion of the representation of phenotypes highlight this year's developments.

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