Download prime

Large-scale phenotyping of aneuploidy mouse models:
Integration of Aneuploidy databases
David Fernández, Ignasi Sahún, Mara Dierssen
Center for Genomic Regulation-Barcelona Biomedical Research Park
Introduction
Website structure
Aneuploidy refers to abnormal copy number of genomic elements, and is
one of the most common causes in morbidity and mortality in human
populations.
The Aneuploidy project has the goals of contributing to the understanding of
the molecular basis and pathogenetic mechanisms of aneuploidies. The
experimental strategies proposed combine technics in human genomics,
mouse models and expression studies. In addition it builds on the
excellence and competitiveness of European laboratories in the field of
aneuploidy.
WP5 website
WP5 website
<admin>
Tissue requests
Mouse models
Tissue collection
Phenotyping
Phenotype
requests
Shared existing
models
Tissue collection
protocols
Phenotyping
Mouse models
Mouse models
DB
Workpackage 5
The goal of WP5 is to make use of mouse models to understand the
phenotypic consequences of gene dosage imbalance and to elucidate the
role of particular chromosomal regions or specific genes in the pathogenesis
of aneuploid syndromes. To this end we perform large-scale phenotyping
(primary and secondary levels) and expression studies.
Tissue collection
Phenotyping DB
Tissue request
Phenotype request
Phenotype DB
Phenotyping
protocols
Services/
Equipment
Website databases
• Mouse models
• Tissue requests
• Phenotyping request
• Phenotype database
Workflow
Mice data: health report,
mice identifiers, date of
birth,...
(experimenter)
Mouse model
description
(experimenter)
Mouse model
Mouse Model DB
New phenotype
request
Website objectives
The objectives of the website is to track WP5 activities so all information
became available through Internet*.
It also provide the web tools to upload the information of mouse models (in
EMMA format) request phenotypical analysis (phenotype request conditions,
mice description, health report, etc.) and tissue requests.
All requests are logged so it’s possible to do WP5 statistics: phenotyping
requests per year, number of tissue requests, etc.
CRG facilities
Key-Obs facilities
Secondary level
results
(Excel file)
Primary level
results
(Excel file)
Web parser
(Java Servlet)
The Phenotypic Database provides the tools for analytical management and
storage of data from the Phenotyping Facilities.
XML*
It allows cross-talk with genomic/transcriptomic/proteomic databases within
the consortium.
WP5 Phenotype
DB
*Data information will be pass protected as needed
Benefits of a website
Information displayed on a website is available from any kind of computer
with an internet connection.
Data can be exchanged between partners in real time.
Analytical processing is satandarized and common ontologies are generated
for all mouse models and phenotyping protocols.
The Aneuploid database is devoted to comparative phenomics in aneuploid
syndromes and will improve our understanding of aneuploidy by combining
the knowledge about phenotypes from mouse models.
Technical information
Key-Obs and CRG provide Excel files associated to a mouse model with
the experiments raw data that are uploaded to the website and then parsed
in a Java Servlet to do summary and statistical levels of visibility.
Once parsed, a mouse model will have an author description, a summary
information, a statistical results and raw data available throught the website.