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MUGEN mouse database; animal models of human immunological diseases.

Aidinis V, Chandras C, Manoloukos M, Thanassopoulou A, Kranidioti K, Armaka M, Douni E, Kontoyiannis DL, Zouberakis M, Kollias G, Mugen NoE consorti - Nucleic Acids Res. (2007)

Bottom Line: Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms.MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes.Database access is free of charge and there are no registration requirements for data querying.

View Article: PubMed Central - PubMed

Affiliation: B.S.R.C. Alexander Fleming, 34 Fleming Street, 16672, Vari, Greece. v.aidinis@fleming.gr

ABSTRACT
The MUGEN mouse database (MMdb) (www.mugen-noe.org/database/) is a database of murine models of immune processes and immunological diseases. Its aim is to share and publicize information on mouse strain characteristics and availability from participating institutions. MMdb's basic classification of models is based on three major research application categories: Models of Human Disease, Models of Immune Processes and Transgenic Tools. Data on mutant strains includes detailed information on affected gene(s), mutant allele(s) and genetic background (DNA origin, gene targeted, host and backcross strain background). Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress and NCBI's Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms. Availability (e.g. live mice, cryopreserved embryos, sperm and ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and Jax/IMSR hyperlinks where available). MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes. Database access is free of charge and there are no registration requirements for data querying.

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Related in: MedlinePlus

Available information on a sample gene of MMdb. Representative view of a gene ‘tumor necrosis factor’ from MMdb, demonstrating basic information for the gene/transgene together with a list of Mugen mice, alleles and MP terms available in MMdb, which are relevant to the particular gene. Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress II and NCBI's Entrez Gene database.
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Figure 2: Available information on a sample gene of MMdb. Representative view of a gene ‘tumor necrosis factor’ from MMdb, demonstrating basic information for the gene/transgene together with a list of Mugen mice, alleles and MP terms available in MMdb, which are relevant to the particular gene. Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress II and NCBI's Entrez Gene database.

Mentions: In addition to providing basic information for the mutant strains, MMdb also offers more detailed features like the DNA origin, targeted and host background, as well as the backcrossing strain and number of backcrosses, thus covering features of the genetic background of the mutant strain (Figure 1). Supplementary strain information, such as the exact strain designation, is provided, together with the JAX or EMMA IDs (where available) in conjunction with the direct links to the respective databases. Furthermore, allelic characteristics are also offered in a separate tab, where the standard allele symbol and name are presented together with the corresponding MGI ID (where available) and the direct link to the MGI database. Moreover, basic information for the gene/transgene, like the gene name, symbol and related chromosome are presented to the user, together with a list of Mugen mice available in MMdb which have a mutation relevant to the particular gene (Figure 2). In addition, each gene/transgene index also includes IDs and direct links to Ensembl [(1) www.ebi.ac.uk/ensembl/], ArrayExpress [(2) www.ebi.ac.uk/arrayexpress/], EURExpress II (www.eurexpress.org/ee/) and NCBI's Entrez Gene [(3) www.ncbi.nlm.nih.gov/sites/entrez?db=gene] databases. Overall, gene, allelic and mutational nomenclature is assigned according to rules and guidelines for mouse genes and strains given by MGI [(4) www.informatics.jax.org/mgihome/nomen/strains.shtml] and based on Gene Ontology (GO) [(5) www.geneontology.org], Mammalian Phenotype (MP) terminology (6–8) and international nomenclature standards.Figure 2.


MUGEN mouse database; animal models of human immunological diseases.

Aidinis V, Chandras C, Manoloukos M, Thanassopoulou A, Kranidioti K, Armaka M, Douni E, Kontoyiannis DL, Zouberakis M, Kollias G, Mugen NoE consorti - Nucleic Acids Res. (2007)

Available information on a sample gene of MMdb. Representative view of a gene ‘tumor necrosis factor’ from MMdb, demonstrating basic information for the gene/transgene together with a list of Mugen mice, alleles and MP terms available in MMdb, which are relevant to the particular gene. Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress II and NCBI's Entrez Gene database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238830&req=5

Figure 2: Available information on a sample gene of MMdb. Representative view of a gene ‘tumor necrosis factor’ from MMdb, demonstrating basic information for the gene/transgene together with a list of Mugen mice, alleles and MP terms available in MMdb, which are relevant to the particular gene. Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress II and NCBI's Entrez Gene database.
Mentions: In addition to providing basic information for the mutant strains, MMdb also offers more detailed features like the DNA origin, targeted and host background, as well as the backcrossing strain and number of backcrosses, thus covering features of the genetic background of the mutant strain (Figure 1). Supplementary strain information, such as the exact strain designation, is provided, together with the JAX or EMMA IDs (where available) in conjunction with the direct links to the respective databases. Furthermore, allelic characteristics are also offered in a separate tab, where the standard allele symbol and name are presented together with the corresponding MGI ID (where available) and the direct link to the MGI database. Moreover, basic information for the gene/transgene, like the gene name, symbol and related chromosome are presented to the user, together with a list of Mugen mice available in MMdb which have a mutation relevant to the particular gene (Figure 2). In addition, each gene/transgene index also includes IDs and direct links to Ensembl [(1) www.ebi.ac.uk/ensembl/], ArrayExpress [(2) www.ebi.ac.uk/arrayexpress/], EURExpress II (www.eurexpress.org/ee/) and NCBI's Entrez Gene [(3) www.ncbi.nlm.nih.gov/sites/entrez?db=gene] databases. Overall, gene, allelic and mutational nomenclature is assigned according to rules and guidelines for mouse genes and strains given by MGI [(4) www.informatics.jax.org/mgihome/nomen/strains.shtml] and based on Gene Ontology (GO) [(5) www.geneontology.org], Mammalian Phenotype (MP) terminology (6–8) and international nomenclature standards.Figure 2.

Bottom Line: Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms.MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes.Database access is free of charge and there are no registration requirements for data querying.

View Article: PubMed Central - PubMed

Affiliation: B.S.R.C. Alexander Fleming, 34 Fleming Street, 16672, Vari, Greece. v.aidinis@fleming.gr

ABSTRACT
The MUGEN mouse database (MMdb) (www.mugen-noe.org/database/) is a database of murine models of immune processes and immunological diseases. Its aim is to share and publicize information on mouse strain characteristics and availability from participating institutions. MMdb's basic classification of models is based on three major research application categories: Models of Human Disease, Models of Immune Processes and Transgenic Tools. Data on mutant strains includes detailed information on affected gene(s), mutant allele(s) and genetic background (DNA origin, gene targeted, host and backcross strain background). Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress and NCBI's Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms. Availability (e.g. live mice, cryopreserved embryos, sperm and ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and Jax/IMSR hyperlinks where available). MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes. Database access is free of charge and there are no registration requirements for data querying.

Show MeSH
Related in: MedlinePlus