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Bioinformatics and Comparative Genomics – WP14
http://www-genoret.u-strasbg.fr/GenoretGenes
L. Poidevin, W. Raffelsberger, R. Reddy, G. Berthommier, N. Gagnière, R. Ripp and O. Poch
Laboratoire de BioInformatique et Génomique Intégratives IGBMC (CNRS – UMR 7104), 1 rue Laurent Fries, Illkirch 67404, Strasbourg France
Abstract: WP14 has developed an automated protocol to retrieve a maximum amount of information for each gene and thus to
characterize retinal genes. This protocol has been applied to the design of the preliminary list of RetChip and validated on an larger
pool of genes (Genoret Genes). To query these information, querying forms have been developed allowing the user to retrieve the
Genoret Gene Identity Card (GIC) by gene name or sequence (blast server). The GIC regroups the general information (gene name,
description, accession number…), external links (MGI, Homologene …) and internal data (Transcriptomic data, EST, MACSIMS,
MAGOS).
In the future, each gene will be characterized by a retinal propensity score. The website will be designed for natural language requests
through the use of our in-house data federative system: BIRD (Biological Integration and Retrieval Data).
Sequence data
Gene related data
Genoret Genes
as
Potential Retinal Genes
MACSIMS
From the Multiple Alignment,
MACSIMS gives a
description of sequence
target according to mined or
propagated genomic,
functional, structural and
evolutionary features
EST Distribution
EST Distribution allows us to
identify tissue(s) where the
gene is expressed.
Phenotyping
Patient data
Animal model
SOPs and
protocols
Transcriptomic analysis (Retinobase)
MACSIMS (Multiple Alignment of Complete Sequence Information Management
System)
Genomic Localization
Genomic localization
allows the analysis of
gene environment,
cytoband features,
calculation of density of
genes for a set of
targets…
Pathways/Networks
‘Omics’ data
Technical characteristics of protocol:
 The protocol is entirely automated and thus easily
reusable.
Retinobase:
- 25 retinal transcriptomic experiments (8 private & 17
public)
- 4 Types of normalisation (dChip, RMA, GenePix, MAS 5.0)
- 2 Types of clustering (Mixture Model and KMeans)
- 4 Organisms (Mouse, Human, Rat, Zebrafis)
 Protocol was created using the programming
languages Tcl and SQL.
The radar display
represents the
expression level of
one gene (through all
probesets) in one
experiment after
each main type of
normalisation (dChip,
RMA).
 Several databases are used to retrieve data:
Ingenuity and KEGG
allow us to retrieve &
compare pathway data
Annotation
GoAnno allows us to
retrieve « enriched »
Gene Ontology for
each gene
3D Models
Magos calculates a
3D model & creates
connexion between
the model and the
MACSIMS data.
When available,
mutations are visible
on sequence & 3D.
Querying :
public databases (UCSC, Affymetrix, NCBI…)
 private databases (Genoret Database, RetinoBase,
Retina cDNA bank…)
 Several software programs are used:
 internal software : GoAnno, MAGOS, MACSIMS, …
 external software : Ingenuity, …
 The automatic protocol has been tested on the
preliminary list of compulsory genes provided by the
members and validated on a larger pool of genes
(Genoret Genes)
 Regular updates of data are performed
 The protocol also allowed us to select the 1500 genes
for RetChip by retrieving genes with the same
expression profile as compulsory genes
Blast Result
Results
By gene name
ImAnno
ImAnno program allows the
owner to annotate ISH images
in order to highlight genes
which are expressed in retina.
Genoret members will have
access to this data through a
simplified display.
cDNA presence
Promoteur analysis
Proteomics
…
Perspectives:
• Improvement of website to simplify and provide a
user-friendly access to gene related data
• A « retinal propensity score »
• Implementation of the BIRD system (Biological
Integration and Retrieval Data) to allow us to answer
questions using a simplified scenario:
• Which mutations correspond to a gene:
Gene -> Mutation -> 3D Model Location
• Which mutations correspond to gene and which
phenotype corresponds to mutation:
Gene -> Mutation -> Phenotype
By sequence
(Blast server)
The user can query our data either by gene name or by sequence.
• If the input gene is already present in our database, the Genoret Gene Identity Card is returned.
• If the input gene is not present in the Genoret Genes Database, the automatic protocol described above is launched
and the Genoret Gene Identity Card is returned
EVI-GENORET Integrated Project LSHG-CT-2005-512036
• Which other genes belong to the same pathway
as my target gene :
Gene -> Pathway -> Others genes in the same
pathway
• Which other genes have the same expression
profile:
Gene -> Clusters of transcriptomic data ->
Other genes in the same cluster