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INTEGRATED FUNCTIONAL GENOMICS IN MUTANT MOUSE MODELS AS TOOLS TO INVESTIGATE THE COMPLEXITY OF HUMAN IMMUNOLOGICAL D

INTEGRATED FUNCTIONAL GENOMICS IN MUTANT MOUSE MODELS AS TOOLS TO INVESTIGATE THE COMPLEXITY OF HUMAN IMMUNOLOGICAL DISEASE (2005 - 2009). 9 European Countries 1 Third Country 14 Research Centers of Excellence 5 Universities 4 SMEs 1 Venture Capital. Integration.

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INTEGRATED FUNCTIONAL GENOMICS IN MUTANT MOUSE MODELS AS TOOLS TO INVESTIGATE THE COMPLEXITY OF HUMAN IMMUNOLOGICAL D

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  1. INTEGRATED FUNCTIONAL GENOMICS IN MUTANT MOUSE MODELS AS TOOLS TO INVESTIGATE THE COMPLEXITY OF HUMAN IMMUNOLOGICAL DISEASE (2005 - 2009) • 9 European Countries • 1 Third Country • 14 Research Centers of Excellence • 5 Universities • 4 SMEs • 1 Venture Capital

  2. Integration Research Training and Spreading MUGEN OBJECTIVES • To systematically study animal models for immune diseases and processes through application of functional genomics platforms. • To integrate the research experience and capacities of each network participant to allow the efficient application of post-genomic approaches to generate new knowledge in immunological diseases and processes. • To ensure spreading of excellence, optimal use and dissemination of the generated knowledge beyond the boundaries of MUGEN partners, by integrating competencies to train researchers and other key staff, to encourage knowledge transfer, to address innovation related aspects, and to raise the public awareness of scientific research issues.

  3. WORK-PACKAGE LIST WP 1: Transgenesis Core WP 7: Innate Immune Activation WP 2: Expression Profiling Core WP 8: Antigen Recognition & Acquired Imm. WP 3 (5): Bioinformatics Core WP 9: Immunological Tolerance WP 4: MUGEN Knowledge Environment WP 10: Intracellular Signaling Cascades WP 5: Relational Databases MMMDb (MDE) WP 11: Infectious Diseases WP 21: Phenotyping Core Integration WP 12: Chronic Inflammation & Autoimmun. Research WP 22: Genotyping Core WP 13: Immune Modulation of Cancer WP 14: Identifying Genetic Susceptibility Training and Spreading WP 15: MUGEN PhD Research School WP 16: MUGEN Mobility Fellowships WP 17: MUGEN Training Courses WP 18: MUGEN Conference WP 19: Management WP 23: MUGEN Awareness & Dissemination

  4. Relational Database (MMMDb - MDE)

  5. Relational Database (MMMDb - MDE) • MMMDb is the MUGEN consortium’s very own virtual on-line mutant mouse strain repository • It is a database whose schema was designed with postgresql and is managed with enterprise java beans (EJBs) technology • It’s interface was developed using xml, jsp, servlets and other java classes

  6. Relational Database (MMMDb - MDE) • MMMDb is acting as a link between MUGEN participating institutions • Simplifies data exchange and submission for researchers • Makes it easy for researchers to share their data with whoever might be interested by switching the dissemination level of their submitted data to Public, thus making data available to all visitors of the MMMDb

  7. Relational Database (MMMDb - MDE) • Various dissemination levels for every single mutant’s data set plus numerous ways of categorizing data for easier sorting (i.e. research application, mutation type, gene affected etc.) • Registered users can submit, edit and even delete their own data by themselves (…of course they cannot edit or delete data submitted by fellow MUGEN participants) • Mutant strains, genes and references are directly linked to other databases (i.e. MGI, ENSEMBL, GENE, PUBMED)

  8. Relational Database (MMMDb - MDE) • The MMMDb is FULLY searchable and EASY to use! • Database can handle all kinds of files (i.e. docs or pdfs for handling and genotyping instructions and also references, images for phenotyping data) • The schema of the database is extremely flexible allowing easy integration of differently structured datasets and adaptation of other data schemas; thus making a first step towards database interoperability and database interconnectivity • A detailed help section for users to be able to make most out of the MMMDb!

  9. Relational Database (MMMDb - MDE) EMMA = 0 IMSR = 0 EMMA = 7 IMSR = 2 EMMA = 4 IMSR = 6

  10. Relational Database (MMMDb - MDE)

  11. Relational Database (MMMDb - MDE)

  12. Relational Database (MMMDb - MDE)

  13. Relational Database (MMMDb - MDE)

  14. Relational Database (MMMDb - MDE)

  15. Relational Database (MMMDb - MDE)

  16. Relational Database (MMMDb - MDE)

  17. Relational Database (MMMDb - MDE)

  18. Relational Database (MMMDb - MDE)

  19. Relational Database (MMMDb - MDE)

  20. Relational Database (MMMDb - MDE)

  21. Relational Database (MMMDb - MDE)

  22. Relational Database (MMMDb - MDE)

  23. Relational Database (MMMDb - MDE) Storing & handling of phenotypic data is currently under development… • As a 1st step we adopted the MGI Mammalian Phenotype Ontology, which has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. • We have built a function to automatically load the MP OBO file from the MGI ftp server in our database • Thus our users can select the most appropriate MP term(s) that suit(s) their mutant from a drop-down list

  24. Relational Database (MMMDb - MDE)

  25. Relational Database (MMMDb - MDE)

  26. Relational Database (MMMDb - MDE)

  27. Relational Database (MMMDb - MDE) • The MMMDb is FULLY searchable and EASY to use! • The schema of the database is extremely flexible allowing easy integration of differently structured datasets and adaptation of other data schemas; thus making a first step towards database interoperability and database interconnectivity • Database can handle all kinds of files (i.e. docs or pdfs for handling and genotyping instructions and also references, images for phenotyping data) • Scheduled links to ArrayExpress (EBI), CAGE database (RIKEN)

  28. INTEGRATED FUNCTIONAL GENOMICS IN MUTANT MOUSE MODELS AS TOOLS TO INVESTIGATE THE COMPLEXITY OF HUMAN IMMUNOLOGICAL DISEASE (2005 - 2009) • 9 European Countries • 1 Third Country • 14 Research Centers of Excellence • 5 Universities • 4 SMEs • 1 Venture Capital

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