ABSTRACT
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
Subject(s)
Biosynthetic Pathways/genetics , Genetic Variation , MicroRNAs/classification , MicroRNAs/genetics , Terminology as Topic , Animals , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Gene Expression Regulation , Humans , Mice , MicroRNAs/metabolism , RNA, Small Cytoplasmic/genetics , RNA, Small Cytoplasmic/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Ribonuclease III/genetics , Ribonuclease III/metabolism , Sequence Analysis, RNA , Transcriptome , ZebrafishABSTRACT
The Mouse Tumor Biology Database (MTB) is designed to provide an electronic data storage, search, and analysis system for information on mouse models of human cancer. The MTB includes data on tumor frequency and latency, strain, germ line, and somatic genetics, pathologic notations, and photomicrographs. The MTB collects data from the primary literature, other public databases, and direct submissions from the scientific community. The MTB is a community resource that provides integrated access to mouse tumor data from different scientific research areas and facilitates integration of molecular, genetic, and pathologic data. Current status of MTB, search capabilities, data types, and future enhancements are described in this article.
Subject(s)
Databases, Factual , Information Storage and Retrieval , Neoplasms, Experimental/pathology , Neoplasms/pathology , Animals , Computational Biology , Disease Models, Animal , Humans , Internet , Mice , Neoplasms/genetics , Neoplasms, Experimental/genetics , User-Computer InterfaceABSTRACT
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
Subject(s)
Databases, Genetic , Genes , Terminology as Topic , Animals , Bibliographies as Topic , Electronic Mail , Genomics , Humans , Information Storage and Retrieval , Internet , Molecular Biology , Proteins/classification , Proteins/genetics , SoftwareABSTRACT
Mice altered by transgenesis or gene targeting ("knockouts") have increasingly been employed as alternative effective tools in elucidating the genetic basis of neurophysiology and behavior. Standardization of specific behavioral paradigms and phenotyping strategies will ensure that these behavioral mouse mutants offer robust models for evaluating the efficacy of novel therapeutics in the treatment of hereditary neurological disorders. The Induced Mutant Resource (IMR) at The Jackson Laboratory (Bar Harbor, Maine, USA) imports, cryopreserves, develops, maintains, and distributes to the research community biomedically valuable stocks of transgenic and targeted mutant mice. Information on behavioral and neurological strains-including a phenotypic synopsis, husbandry requirements, strain availability, and genetic typing protocols-is available through the IMR database (http://www.jax.org/resources/documents/imr/). A current catalog of available strains is readily accessible via the JAX Mice Web site at http://jaxmice.jax.org/index.shtml. In addition, The Jackson Laboratory is now home to TBASE (http://tbase.jax.org/), a comprehensive, community database whose primary focus is on mouse knockouts. TBASE accommodates an exhaustive bibliographical resource for transgenic and knockout mice and provides a detailed phenotypic characterization of numerous behavioral knockouts that is primarily extracted from the literature. Concerted efforts to merge the two resources into a new, schematically reformed database are underway.
Subject(s)
Behavior, Animal/physiology , Mice, Knockout/genetics , Mice, Transgenic/genetics , Phenotype , Animals , Brain/physiology , Catalogs as Topic , Databases, Genetic , Genetics , Internet , MiceSubject(s)
Databases, Factual , Genes/genetics , Genome , Animals , Computational Biology/methods , Information Storage and Retrieval , MiceABSTRACT
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 provides standard nomenclature and consensus map positions for mouse genes and genetic markers; it provides a curated set of mammalian homology records, user-defined chromosomal maps, experimental data sets and the definitive mouse 'gene to sequence' reference set for the research community. The integration and standardization of these data sets facilitates the transition between mouse DNA sequence, gene and phenotype annotations. A recent focus on allele and phenotype representations enhances the ability of MGD to organize and present data for exploring the relationship between genotype and phenotype. This link between the genome and the biology of the mouse is especially important as phenotype information grows from large mutagenesis projects and genotype information grows from large-scale sequencing projects.
Subject(s)
Databases, Factual , Genome , Mice/genetics , Alleles , Animals , Genetic Markers , Internet , Mice, Inbred Strains , Sequence AlignmentABSTRACT
The Mouse Tumor Biology (MTB) Database serves as a curated, integrated resource for information about tumor genetics and pathology in genetically defined strains of mice (i.e., inbred, transgenic and targeted mutation strains). Sources of information for the database include the published scientific literature and direct data submissions by the scientific community. Researchers access MTB using Web-based query forms and can use the database to answer such questions as 'What tumors have been reported in transgenic mice created on a C57BL/6J background?', 'What tumors in mice are associated with mutations in the Trp53 gene?' and 'What pathology images are available for tumors of the mammary gland regardless of genetic background?'. MTB has been available on the Web since 1998 from the Mouse Genome Informatics web site (http://www.informatics.jax.org). We have recently implemented a number of enhancements to MTB including new query options, redesigned query forms and results pages for pathology and genetic data, and the addition of an electronic data submission and annotation tool for pathology data.
Subject(s)
Neoplasms, Experimental/pathology , Neoplasms/pathology , Animals , Databases as Topic , Disease Models, Animal , Humans , Information Services , Internet , Mice , Neoplasms/genetics , Neoplasms, Experimental/geneticsABSTRACT
The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.
Subject(s)
Databases, Factual , Gene Expression Profiling , Mice/genetics , Animals , Information Services , InternetABSTRACT
We are building a framework map of known-order anchor markers between the mouse T31 radiation hybrid (RH) panel and the recombination map based on The Jackson Laboratory (TJL) interspecific backcross panels using the established genetic order to evaluate and strengthen the RH results. In making this map comparison, we have elucidated several problems inherent in RH mapping and minimized these by careful attention to data gathering and interpretation methods. We describe lessons and pitfalls of developing radiation hybrid maps, using the example of mouse Chromosome 18, for which we have built a framework map of microsatellite anchor loci spanning the entire chromosome at significant LOD with no gaps. Sixty-five D18Mit- simple sequence length polymorphism (SSLP) markers form a continuous linkage along the T31 RH Chromosome 18 (RH map length 1598 cR, genetic length 41 cM) with all LODs greater than 6. These markers are also placed on TJL interspecific backcrosses, and the order of the markers in the two systems is in complete agreement. We are continuing to cross-reference the RH data to TJL backcross data for the other mouse chromosomes to improve further the power of RH mapping and to integrate more precisely the extensive existing recombination mapping data for the mouse with the incoming radiation hybrid map data.
Subject(s)
Chromosome Mapping , Crosses, Genetic , Radiation Hybrid Mapping , Recombination, Genetic/genetics , Alleles , Animals , Chromosomes/genetics , Cricetinae , DNA/genetics , DNA Primers , Female , Hybrid Cells , Male , Mice , Mice, Inbred C57BL , Microsatellite Repeats , Muridae , Polymerase Chain Reaction , Reproducibility of ResultsABSTRACT
A community-wide effort to establish baseline phenotypic data on commonly used and genetically diverse inbred mouse strains and to provide the information through a publicly accessible database.
Subject(s)
Genome , Mice, Inbred Strains/genetics , Animals , Databases as Topic , Mice , PhenotypeABSTRACT
For effectively annotated phenotypes for mouse, a number of detailed phenotypic classification systems are needed. The rapidly increasing number of phenotypically described characteristics of both normal and mutant mice are providing a rich data set for comparison and analysis. However, we cannot rely on text descriptions that are subject to the word-usage style of the writer if we are to do large-scale comparative analysis of traits and diseases. The rationale for developing vocabularies and examples of several vocabularies being developed are described. Finally, the critical nature of community participation in both building and applying phenotype vocabularies is discussed.
Subject(s)
Algorithms , Mice/genetics , Mutation , Terminology as Topic , Animals , Databases, Factual , Internet , PhenotypeABSTRACT
The Mouse Genome Database supports the use of mice in genome research, offering researchers information on gene characterization, genetic maps, comparative genomic data, and phenotypes.
ABSTRACT
The mouse is a prime organism of choice for modelling human disease. Over 450 inbred strains of mice have been described, providing a wealth of different genotypes and phenotypes for genetic and other studies. As new strains are generated and others become extinct, it is useful to review periodically what strains are available and how they are related to each other, particularly in the light of available DNA polymorphism data from microsatellite and other markers. We describe the origins and relationships of inbred mouse strains, 90 years after the generation of the first inbred strain. Given the large collection of inbred strains available, and that published information on these strains is incomplete, we propose that all genealogical and genetic data on inbred strains be submitted to a common electronic database to ensure this valuable information resource is preserved and used efficiently.
Subject(s)
Mice, Inbred Strains/genetics , Animals , Databases, Factual , Disease Models, Animal , Humans , Internet , Mice , PhenotypeABSTRACT
The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www. informatics.jax.org). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional information about the laboratory mouse. MGD scientists and annotators work cooperatively with the research community to provide an integrated, consensus view of the mouse genome while also providing experimental data including data conflicting with the consensus representation. Recent improvements focus on the representation of phenotypic information and the enhancement of gene and allele descriptions.
Subject(s)
Databases, Factual , Genome , Animals , Genetic Markers , Internet , Mice , Terminology as TopicABSTRACT
The Mouse Tumor Biology Database (MTB) is a Web-based resource that provides access to information on tumor frequency and latency, genetics and pathology in genetically defined mice (transgenics, targeted mutations and inbred strains). MTB is designed to serve as an information resource for cancer genetics researchers who use the laboratory mouse as a model system for understanding human disease processes. Data in MTB are obtained from the primary scientific literature and direct submissions by the research community. MTB is accessible from the Mouse Genome Informatics Web site (http://www. informatics.jax.org). User support is available for MTB via Email at mgi-help@informatics.jax.org
Subject(s)
Databases, Factual , Neoplasms, Experimental/genetics , Neoplasms, Experimental/pathology , Animals , Internet , Mice , Mice, Inbred Strains , Mice, Mutant Strains , Mice, TransgenicABSTRACT
The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. The database is designed as an open-ended system that can integrate different types of expression data. New expression data are made available on a daily basis. Thus, GXD provides increasingly complete information about what transcripts and proteins are produced by what genes; where, when and in what amounts these gene products are expressed; and how their expression varies in different mouse strains and mutants. GXD is integrated with the Mouse Genome Database (MGD). Continuously refined interconnections with sequence databases and with databases from other species place the gene expression information in the larger biological and analytical context. GXD is accessible through the Mouse Genome Informatics Web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtm l
