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Genomics

Approach. Component examined. Techniques. Genomics. Genes. Sequencing Programs. DNA arrays GeneChip. Transcriptomics. mRNA. 2D PAGE MALDI-MS ESI-MS. Proteomics. Proteins. Metabolomics. Metabolites. GC-MS.

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Genomics

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  1. Approach Component examined Techniques Genomics Genes Sequencing Programs DNA arrays GeneChip Transcriptomics mRNA 2D PAGE MALDI-MS ESI-MS Proteomics Proteins Metabolomics Metabolites GC-MS

  2. mRNA level  expressed protein level nor does it indicate the nature of the functional protein product Functional Protein Product Genomic Sequence Protein Product mRNA Translational Control Post-Translational Control Transcriptional Control

  3. t t t Gene Expression Protein Temporal Changes in mRNA and protein When you measure expression affects what you find

  4. 1000 1000 100 100 x 10 10 mRNA (EST clones) Lung Ovarian CNS Leukemia Renal Melanoma Breast mRNA (Northern) x x x x x 1 1.0 R=0.48 R = 0.43 0.1 0.1 0.1 1 10 100 0.1 1.0 10 100 Protein (Affinity-HPLC) Protein (2D gels) Does mRNA level correlate with protein level? 20 liver proteins and corresponding mRNAs Glutathione-S-transferase in 60 human cell lines Anderson & Anderson Electrophoresis 1998 19:1853-1861 From Tew et al 1996 Anderson & Seilhamer Electrophoresis 1997 18:533-537

  5. Challenges of proteins vs DNA DNA Protein • Static • Can be amplified • Little complexity: Single component • Good solubility characteristics • Very dynamic • Cannot be amplified • Very complex: post-translational modification • Variable solubility

  6. Identifying new protein complexes: Isolation of proteins using: Classical Purification +1D PAGE Tag Purification +1D PAGE

  7. Phenotypic Complexity of the Eukaryotic Proteome Domain Expansion Somatic Evolution Domain Accretion • Duplication • Divergence • Recombination Recombination Protein Architecture Paralogous Expansion Somatic Rearrangement Horizontal Transfer Protein Diversity Alternative Splicing Modifications Functional Diversity Protein Interactions Systems de novo Biological Processes

  8. Eukaryotic Proteomes Proteome Human Fly Worm Yeast Mustard Weed Number of Genes 31,778 13,338 18,266 6,144 25,706 % of DB Matches* 51 56 50 50 52 (* Similarity search of protein sequences in the database)

  9. Comparative Analysis of Proteomic Pheno-Complexity Functional Diversity Eubacteria Protein Diversity Eukarya Domain Accretion Protein Architecture Archaea Unicelluar Organisms Invertebrates Vertebrates Mammals Human Lineage- Specific Proteins Vertebrate- Specific Proteins Conserved Core Proteins

  10. Protein Sequence Homology (1) Protein Match with Known or Unknown Function Query Match (2) Domain Match with Known or Unknown Function Query Match Ortholog:A evolutionarily conserved gene that arose during speciation Paralogs:Genes that arose due to intra-genome duplication in a species

  11. Protein Sequence Comparison (I) Homology • > 40 % : Same Function • 25-40 % : Similar Function • < 25 % : Different Function (II) Distance • Phylogenetic Tree

  12. Comparative Proteomics Domain/Protein* Yeast Worm Fly Weed Human Eukaryote-specific 1 1 1 1 1 0 1 1 1 1 Metazoan-specific 0 1 1 0 1 Animal-specific 0 0 0 0 1 Vertebrate-specific *: The domain/protein is present (1) or absent (0) in the proteome.

  13. Eukaryotic Proteomes Shared with Humans Human 61% 43% Fly Worm 46% Yeast

  14. Conserved Core Groups in Eukaryotes Human (3,109 Proteins) Fly (1,445 Proteins) Yeast (1,441 Proteins) Conserved Core Proteins in 1,308 Groups Worm (1,503 Proteins)

  15. Vertebrate-specific Proteins Unicelluar Organisms Invertebrates Vertebrates Mammals Human Human 22% Vertebrate- Specific Proteins 21% Eukaryote and Prokaryote 32% 24% Other Eukaryotes And Animals Vertebrates and Other Animals

  16. Comparative Pheno-Complexity Functional Diversity Bacteria Protein Diversity Eukarya Domain Accretion Protein Architecture Archeae Unicelluar Organisms Invertebrates Vertebrates Mammals Human Vertebrate- Specific Proteins Conserved Core Proteins Lineage- Specific Proteins • Housekeeping Functions • Engery/Metabolism • DNA replication/Repair • Translation • Physiological Differences • Defense & Immunity • Cell-Cell Communications • Nervous System

  17. Protein Diversity in Eukaryotes • Horizontal Gene Transfer • Invention of Protein Domain • Expansion of Protein/Domain Families • Evolution of New Protein Architectures

  18. Lateral Gene Transfer Bacteria Human 223 Genes • Hydrolase • Oxidoreductase • Dehydrogenase • Monoamine Oxidase • Transporter • Lineage Specific • Intron Acquisition

  19. Comparative Pheno-Complexity Functional Diversity Bacteria Protein Diversity Eukarya Domain Accretion Protein Architecture Archeae Unicelluar Organisms Invertebrates Vertebrates Mammals Human Vertebrate- Specific Proteins Conserved Core Proteins Lineage- Specific Proteins • Housekeeping Functions • Engery/Metabolism • DNA replication/Repair • Translation • Physiological Differences • Defense & Immunity • Cell-Cell Communications • Nervous System

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