Respective contributions of MIAME, GeneOntology and UMLS for transcriptome analysis

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Respective contributions of MIAME, GeneOntology
and UMLS for transcriptome analysis

• Fouzia Moussouni, Anita Burgun, Franck Le Duff,
• Emilie Guérin, Olivier Loréal
• INSERM U522 and Medical Informatics Laboratory,
• CHU Pontchaillou
• Rennes, FRANCE

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Transcriptome DNA microarray study of
transcriptionnal response of the cell
Normal
Pathologic
Response to chemics or foods treatment
Response to a growth factor
Response to genetic disturbances
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Pathological situations studied at INSERM U522
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One may deposit thousands of genes
Intensive data generation
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One gene but multiple descriptions

• Nucleic Sequence components - promoters,
  introns, exons, transcripts, regulators,
• Chromosomal localization,
• Functional proteins and known genes products,
• Tissue distribution,
• Known gene interactions,
• Expression level in physiologic and pathologic
  conditions,
• Known gene variations,
• Clinical Implications,
• Literature and bibliographic data on a gene.

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Need of an integrated gene expression environment
(for the liver!)
External Sources
Clinical Data
experimental data
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Knowledge extraction and data exchange
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Standardization ONTOLOGY DESIGN
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MIAME
MIAME will provide a standard framework to
represent the minimum information that must be
reported about microarray experiments

• Experience
• Array
• Samples
• Hybridization
• Measures
• Normalisation and control

Work in progress ...
Minimum information about a microarray experiment
(MIAME) toward standards for microarray data', A.
Brazma, at al., Nature Genetics, vol 29 (December
2001), pp 365 - 371.
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GeneOntology (GO)
GO is an ontology for molecular biology and
Genomics,
But GO is not populated with

• gene sequences
• gene products, ...

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UMLS

• The Unified Medical Language System
• (UMLS) is intended to help health professionals
  and researchers to use biomedical information
  from different sources.

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• Examples from iron metabolism are studied
• How pathologic disease states related to iron
  metabolism alteration are described in GO and
  UMLS ?

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BIOLOGICAL MODEL FOR IRON METABOLISM
IRON METABOLISM GENES
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Iron overload due to a gene alteration
Iron overload during Aceruloplasminemia
NO
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BIOLOGICAL MODEL FOR IRON METABOLISM
IRON METABOLISM GENES
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A second scenario related to iron metabolism
genes alteration
Cataract and hyperferritinemia
mRNA
L_Ferritin
CATARACT and HYPERFERRITINEMIA !
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UMLS view
Cataract and hyperferritinemia
AA, Peptide or Prorein Biologically Active
Substance
Ferritin
AA, Peptide or Protein
Co-occurs In Medline
IRE
Co-occurs In Medline (freq 26)
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GO/ GOAnnotations view
Cataract and hyperferritinemia
Link in GO Annotations DB
Ferritin Heavy Chain
IRP
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Target representation
Cataract and hyperferritinemia
Hyperferritinemia
Genes Mutated genes
IRP
Cataract
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And more generally Recapitulative
UMLS
MIAME
We need precise and dynamic models to get the
whole picture
GOA
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(No Transcript)
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Gene products for Iron metabolism, as they are
actually described in GO and UMLS.