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Lesson 13

Lesson 13. Functional Genomics II: Functional Databases and Clustering. Functional Genomic Databases. Gene Ontology - Protein Function BIND - Protein Interactions (Biomolecular Interactions Network Database) KEGG - Biological Pathways

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Lesson 13

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  1. Lesson 13 Functional Genomics II: Functional Databases and Clustering

  2. Functional Genomic Databases Gene Ontology - Protein Function BIND - Protein Interactions (Biomolecular Interactions Network Database) KEGG - Biological Pathways (Kyoto Encyclopedia of Genes and Genomes)

  3. Tyrosine Kinase Function

  4. c-src Function SH2 - Bind phosphotyrosines SH3- Bind proline-rich regions Kinases - attach phosphates to other molecules

  5. c-Src Equivalent Logic Gate Input Output SH3 Bound Kinase Phosphorylated Src Kinase Activity SH2 Phosphorylated

  6. c-Src: A Biological Microchip

  7. Tyrosine-kinase transmembrane receptors

  8. Src family tyrosine-kinase binding

  9. Two types of src • c-src (cellular src: native to eucaryotic genome) • v-src (viral src: rouse sarcoma virus) v-src infects vertebrate cells and helps cause cancer.

  10. PDGF-Platelet Growth FactorPDGFR-Platelet Growth Factor Receptor Binding

  11. SRC family proteins bind to PDGFR

  12. SH2/SH3 Adaptor Proteins

  13. Gene Ontology Ontology- Classification scheme  Being - Word

  14. Gene Ontology Classifications 3 Protein classification schemes: 1. Biological Process - What it does 2. Molecular Function- How it does it 3. Cellular Component- Where it does it

  15. Trees Child 1 Parent A Child 2 Child 3 Parent B Child 4 A child may have only one parent

  16. Directed Acyclic Graphs Child 1 Parent A Child 2 Child 3 Parent B Child 4 A child may have more than one parent

  17. Gap Junctions

  18. Gap Junction Channels

  19. Connexons and Connexins

  20. Hierarchical Clustering: Distances

  21. Hierarchical clustering-Dendrogram and heat map

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