DomainGraph – visual analysis of the biological effects of alternative splicing

1. DomainGraph – visual analysis of the biological effects of alternative splicing

2. Introduction • Affymetrix Exon Array enables researchers to: • Identify / classify occurrences of alternative splicing events • Identify protein isoforms occurring in specific tissues • Identify protein isoforms occurring in diseased tissues • Focus mainly on identification of alternative splicing events and isoforms • But: what about the biological impact?

3. Introduction Protein – Protein interaction: PDB entry: 1OPH Alpha-1-antitrypsin (red), P01009 Cationic trypsin (yellow), P00760 Serin Protease Inhibitor (red), PF00079 Trypsin (yellow), PF00089 • Domain definition: • structural units of proteins • fold independently • specific functions • may appear in several proteins • Domain – Domain interaction: • underlies protein interaction

4. Introduction • Alternative Splicing Affymetrix Technical Note: Identifying and Validating Alternative Splicing Events PDB entry: 1OPH

5. DomainGraph 3.0 • Cytoscape plugin • Main functionalities: • I.) Analysis of AltAnalyze statistics (without prior biological knowledge) • a) Gene / Transcript / Protein / Functional Groups Analysis • b) Pathway Analysis • II.) Analysis of specific interaction networks • a) Visualization of protein interaction networks with underlying domain interactions • b) Visualization of gene interaction networks and their encoded proteins with domain composition • c) Integration of AltAnalyze statistics

6. DomainGraph Visualization • Graph representation of genes, proteins, and domains and their connections • Nodes: • Genes • Proteins • Domains • Edges: • Gene interactions • Protein interactions • Domain interactions • Gene – protein linker • Protein – domain linker Node Edge (undirected)

7. AltAnalyze and DomainGraph Overview

8. I.) Analysis of AltAnalyze results (no prior biological knowledge of the data needed)

9. I.) Analysis of AltAnalyze statistics – Table View

10. I.) Analysis of AltAnalyze statistics – Gene / Gene Product Analysis Single-Gene Network View Probeset View

11. I.) Analysis of AltAnalyze statistics – Single-Gene Network View Domain Node Protein Node (regulated) Domain Node (regulated) Gene – protein linker Gene Node (regulated) Protein – domain linker Protein Node

12. I.) Analysis of AltAnalyze statistics – Probeset View Gene: FYN Protein, domain Exon structure Probesets, miRNA-BS

13. II.) Analysis of a specific network – Probeset View

14. I.) Analysis of AltAnalyze statistics – Table View

15. I.) Analysis of AltAnalyze statistics – Pathway Selection

16. I.) Analysis of AltAnalyze statistics – Pathway View Regulated Genes: green WikiPathway Import via GPML-Plugin

17. II.) Analysis of a specific network a) Creating a Domain Graph

18. II.) Analysis of a specific network – PPI network • Network annotated with protein IDs: • Decomposition of proteins into constituent domains • Inference of domain-domain interactions (DDIs) • Visualization of protein interactions with constituent domains and DDIs • Focus on DDIs forming the PPIs • DDI datasets provided with DomainGraph • From PDB structures: iPfam, 3did • From predictions: InterDom, DPEA, DIMA,…

19. II.) Analysis of a specific network – PPI network • Input: • Protein interaction network • Selection of DDI dataset • Selection of initial view (more or less detailed) • Identifier specification (Ensembl, UniProt) • Internal Computation: • Decomposition of proteins into domains • Calculation of domain interactions • Calculation of initial view • Output: • Domain Graph with protein and domain nodes; protein and domain interactions; protein – domain linkers

20. II.) Analysis of a specific network – PPI network

21. PPI network Protein interaction with confidence score Domain interaction with confidence score Protein node Domain node Protein domain linker

22. PPI network • Network Views: • Extended view • Displays domains for each protein separately • Relatively high number of nodes and edges • Compact view • Identical domains occurring in different proteins are merged • Decreased number of nodes and edges • Protein network view • Display domain interactions for user-selected proteins only • Stepwise exploration of network possible

23. Features: Protein and Domain Annotations

24. II.) Analysis of a specific network – GGI network • Network annotated with gene IDs: • Extraction of protein isoforms encoded by the genes • Decompositions of protein isoforms into constituent domains • Visualization of gene interaction with encoded proteins and constituent domains • Focus on protein isoforms and their differences

25. II.) Analysis of a specific network – PPI network • Input: • Gene interaction network • Selection of initial view (more or less detailed) • Identifier specification (Ensembl, Entrez) • Internal Computation: • Extraction of all protein isoforms encoded by the genes • Decomposition of protein isoforms into domains • Calculation of initial view • Output: • Domain Graph with gene, protein and domain nodes; gene interactions; gene – protein and protein – domain linkers

26. II.) Analysis of a specific network – GGI network

27. GGI network Protein – domain linker Gene – protein linker Gene node Gene interaction Protein node Domain node

28. II.) Analysis of a specific network – Domain and Exon Structure Comparison Gene: FYN

29. II.) Analysis of a specific network b) Integrating AltAnalyze Statistics

30. II.) Analysis of a specific network – AltAnalyze Data Integration • Input: • Domain Graph built from PPI or GGI network • AltAnalyze probeset statistics file • Internal Computation: • Mapping probesets to proteins, exons, domains, miRNAs • Calculating positions of regulated probesets • Output: • Domain Graph with gene, protein, and domain nodes highlighted according to occurrences of alternative splicing

31. II.) Analysis of a specific network – Domain Graph with Integrated AltAnalyze Data

32. Domain Graph with Integrated AltAnalyze Data Gene Node (regulated) Protein Node (regulated) Domain Node (regulated)