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Overview

Overview. Introduction Biological network data Text mining Gene Ontology Expression data basics Expression, text mining, and GO Modules and complexes Domains and conclusion. Domain Interaction networks. Protein domain basics Applications of domain interaction networks

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Overview

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  1. Overview • Introduction • Biological network data • Text mining • Gene Ontology • Expression data basics • Expression, text mining, and GO • Modules and complexes • Domains and conclusion

  2. Domain Interaction networks • Protein domain basics • Applications of domain interaction networks • Inferring domain interaction networks • Domain interaction networks in Cytoscape.

  3. Protein structures are built from domains. Domain composition implies protein function. Facts about protein structure

  4. Protein domains come in families

  5. Domains can be recognized through sequence similarity Source: http://www.sbg.bio.ic.ac.uk/ people/rob/sf/sf.html

  6. Interactions are often domain-specific Source: http://faculty.umdnj.edu/ cabm/faculty_stock.asp

  7. Why study protein domain interactions? • A putative protein-protein interaction is more reliable if the proteins have domains that might interact. • If something disrupts the protein sequence, it might disrupt the domain, and thus the network • Genetic or somatic mutations • Splice variation

  8. Transcription Pre-mRNA Splicing mRNA Translation Protein Exon Exon Exon Intron Intron Intron Exon DNA

  9. Single Protein-Protein Interaction

  10. UBL UBA XPC UBA Structural Protein Domain Architecture

  11. Which part of the proteins interact? • Protein structure: which domain structures are complementary? • Domain co-occurrence: which domains tend to appear in the same proteins? • Rosetta stone: are any domains fused in other proteins? • Yeast two-hybrid domain interactions: coming soon.

  12. UBL UBA XPC UBA ! Josephin UIM UIM Databases such as InterDom provide putative interactions of Pfam domains Which part of these proteins interact?

  13. Domain interaction networks

  14. For this hands-on session • Explore usage of the Cytoscape Domain Network builder plugin • Fill out your evaluation sheets.

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