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


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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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slide1

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
mugen objectives

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.
work package list
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

relational database mmmdb mde1
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
relational database mmmdb mde2
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
relational database mmmdb mde3
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)
relational database mmmdb mde4
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!
relational database mmmdb mde5
Relational Database (MMMDb - MDE)

EMMA = 0

IMSR = 0

EMMA = 7

IMSR = 2

EMMA = 4

IMSR = 6

relational database mmmdb mde19
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
relational database mmmdb mde23
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)
slide28

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