committee :l. chiche (cbs), o. gascuel (lirmm), m.-p. lefranc (igh) and : cirad, crbm, gpi, ibp,...
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Committee : L. Chiche (CBS), O. Gascuel (LIRMM), M.-P. Lefranc (IGH)
And : CIRAD, CRBM, GPI, IBP, IGMM, ISEM, LDCC
Montpellier has an high research potential in Bioinformatics:
More than 50 researchers, PhDs and post-doctoral students
Internationally recognized programs, databases and servers: BIONJ, PHYLOWIN, IMGT, ESTHER, DOMO, BIOSERV, STAR …
National and international responsibilities, e.g. Chair of ACI IMPBio.Thanks to the Genopole:
10 within Genopole collaborations supported by French programs
A master (DESS) in Bioinformatics
Bioinformatics seminars (2/month) and events (eg, Transcriptome Statistical Analysis, 110 attendees, 2002).
Bioinformatics Montpellier GenopoleJournées "Bioinformatique des Génopoles"
Lyon, 22-23 octobre 2003
Three main axes
IMGT
Structural Bioinformatics (protein structure prediction, structural domain clustering, NMR spectra analysis, Knottin database)
Comparative genomics (phylogeny, sequence analysis, alignment)
Perspectives:
Developing IMGT and structural servers and databases
Spreading our software
Designing new dedicated servers (e.g., transcriptome interpretation)
Providing courses on software
Incentive policy towards “young teams”
Bioinformatics Montpellier Genopole
IMGT, the international reference
in Immunogenetics and Immunoinformatics
IMGT,a CNRS registered trademark
EU, Canada, USA
RIO Platform 2001
NetWatch of Science 2002
IMGT,an European flagship
(BIOMED1, BIOTECH, 5th PCRDT)
IMGT, a common access
to standardized, expertly annotated
and integrated data
IMGT, uniqueNo equivalent in Japan
and in USA
IMGT, the international ImMunoGeneTics information system ® http://imgt.cines.fr
Coordinator: Marie-Paule LEFRANC
IMGT specialized in
Immunoglobulins (IG) (antibodies)
T cell receptors (TR)
Major histocompatibility
complex (MHC)
The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
IMGT domain of research: the adaptive immune system
Immunoglobulin
B cellT cell
T cell Receptor MHC
peptide
Trimolecular complex
Immunoglobulin and T cell receptor synthesis
2 x 10 12
5' 3'
V D J C
39- 46 x 23 x 6 34 - 37 x 5 Kappa 30- 33 x 4 -5 Lambda
5' 3'
V J C
250HEAVY CHAIN LIGHT CHAIN
5' 5'3' 3'x 1000
6300 POTENTIAL RECOMBINATIONS POTENTIAL RECOMBINATIONS
N REGIONS AND SOMATIC MUTATIONS
ABOUT POSSIBILITIES3.5 x 10 5ABOUT POSSIBILITIES6.3 x 10 6
185 +165
FUNCTIONAL GENES
DIFFERENT ANTIBODIES
The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
5 Databases
Sequence databases
IMGT/LIGM-DB 77,463 IGand TR nucleotide sequences fromhuman and 150 other vertebrate species, on the Web since July 1995
IMGT/PRIMER-DB on theWeb since 2000
IMGT/MHC-DB hosted at EBI
Genome database
IMGT/GENE-DB1375 IG and TR genes and 2201alleles from human and mouse, on
the Web since February 2003
3Dstructure database
IMGT/3Dstructure-DB634 structures of IG, TR and MHC
Web Resources
Sequences
Alignments of alleles
Tables of alleles
Protein displays, etc.
Genome
Chromosomal localizations Locus representationsGene tables, etc.
2D and 3D structures
2D Colliers de Perles3D representations, etc.
Sequence analysis
• IMGT/V-QUEST
• IMGT/JunctionAnalysis
• IMGT/PhyloGene
• IMGT/Allele-Align
Genome analysis
• IMGT/GeneSearch• IMGT/GeneView• IMGT/LocusView
3D structure analysis
• IMGT/StructuralQuery
8 Tools on line
IMGT Repertoire
8000 HTML pages!
http://imgt.cines.fr
IMGT-ONTOLOGY has been developedto share, reuse and represent knowledge in immunogenetics
IMGT-ONTOLOGY covers five main concepts:
IMGT-ONTOLOGY
IDENTIFICATION
DESCRIPTION
CLASSIFICATION
OBTENTION
http://imgt.cines.fr
NUMEROTATION
"CLASSIFICATION" concept
The "CLASSIFICATION" concept organizes the immunogenetics knowledge useful to name and classify IG and TR genes in IMGT. (A) Concepts of classification and their
relations. (B) Examples of instances: for each concept of classification is shown the instance which allows the classification of the human IGLV2-11*02 allele.
group
subgroup
allele
locus
is a member of an instance of
is a member of an instance of
is a variant of an instance of
is ordered in an instance
of
IGLV
IGLV2
IGLV2-11
IGLV2-11*02
human IGL(22q11.1-q11.2)
is ordered in
is a member of
is a variant of
is a member of
A B
gene
http://imgt.cines.fr
The international ImMunoGeneTics databaseCoordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
V-GENE
V-EXON
FR1-IMGT FR2-IMGT FR3-IMGT
L-PART1
V-REGION
CC5 ’UTR 3 ’UTR
CD
R3
-IMG
T
DONOR-SPLICE
W
V-GENE V-EXON
FR3-IMGT CDR3-IMGT
L-PART1 DONOR-SPLICE
V-REGION FR1-IMGT
Label 1 Label 2
V-REGION CDR3-IMGT
Label relations
"DESCRIPTION" concept
The "OBTENTION" concept specifies the origin and methodology
"OBTENTION" concept
libraries- genomic- cDNA-combinatorial
origin methodology
transgenic- animal- plant
PCR
cell, tissue, organ- PBL- liver
autoimmune diseases- autoantibody- rheumatoid factor
clonal expansion diseases- leukemia- lymphoma- myeloma
hybridoma- monoclonal antibody
http://imgt.cines.fr
IMGT-ML Schema
IMGTOntologyIMGTOntology
IdentificationIdentification
imgtimgt
NumerotationNumerotation
ObtentionObtention
ClassificationClassification
IMGTDataIMGTData
knowledgeknowledge
seqDataseqData
DescriptionDescriptionExternal schemaExternal schema
http://imgt.cines.fr
IMGT-ML Architecture
XML SchemaXML Schema
IMGT-ONTOLOGY
Documentation
DatabasemodellingDatabasemodelling
ControlledvocabularyControlledvocabulary
Data distribution
format
Data distribution
formatBiologicalexpertize
Biologicalexpertize
http://imgt.cines.fr
2. Services
• WWW at Montpellier: 180,000 sites since January 2000 140,000 requests per month• Data distribution by FTP: CINES, IGH, INFOBIOGEN, EBI• Many sites SRS: INFOBIOGEN, EBI, Institut Pasteur, ... and EMBnet nods• Search by BLAST and FASTA: on different servers (INFOBIOGEN, EBI, etc.)• IMGT Bloc-notes: IMGT Immunoinformatics page, numerous hyperlinks to external sites
The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
1. Research and development
52 publications 1 chapter "Consanguinity" in Encyclopedia of Genetics 20012 books: The Immunoglobulin FactsBook, Academic Press, 2001
The T cell receptor FactsBook, Academic Press, 200147 communications27 invited conferences (China, Japan, USA, Belgium, Italia, The Netherlands, UK)2 PhD theses (1 tenure job at CIRAD, 1 postdoctorate at Princeton, USA)
collaborations USA, Canada, China, Russia, Lebanon, UK, Belgium (EUROGENTEC)
2000-2003 IMGT Platform
IMGT platform
3. Education Participation to the creation of the:• DESS Bioinformatics: Université Montpellier II, 2001• Bioinformatics modules: Doctoral School CBS2, Montpellier, 2001 Doctoral School Univ. St-Joseph, Beirut, Lebanon, 2002 University of Monastir, Tunisia, 2003
4. Innovations, normes et standards
IMGT-ONTOLOGY, the first and only ontology in immunogenetics and immunoinformaticsIMGT Scientific chart provides the controlled vocabulary and the annotation rules• IMGT nomenclature approved by the Human Genome Organization (HUGO) Nomenclature Committee (HGNC) in 1999, 673 human genes and 1206 alleles. The only example of delegation by HGNC. • direct links from LocusLink NCBI to IMGT. The only example of direct links from NCBI to an external site • In development: XML and IMGT-ML, Web-Services, Data integration in medical informatics.
The international ImMunoGeneTics information system®Coordinator: M.-P. Lefranc, Montpellier, France http://imgt.cines.fr
.
Genome diversity developmental and comparative immunology, evolution of the
adaptive immune system
Biotechnology and antibody engineering
chimeric, humanized, human antibodiesin transgenic mice, scFv combina-
torial libraries, intrabodies
Veterinary researchrepertoire in farm
and wild animal species
Medical researchrepertoire in normal and pathological
situations, autoimmune diseases, AIDS, leukemias, lymphomas, myelomas,
residual diseases, etc.
Therapeutical approaches immunotherapy, grafts,
immunomodulation, immunosppression
IMGT, the international ImMunoGeneTics information system® http://imgt.cines.fr
Coordinator : Marie-Paule LEFRANC
IMGT, a team of
21 persons:
8 CDD annotators
(5 EU, 1 EUROGENTEC
1 Genopole, 1 PPF)
4 Permanent staff
(UM2: 1.5 PU, 0.5 IE
CNRS: 1 IE, 1 ITA)
9 Students (3 PhD,
6 for 4 months/a year)