1. Session outline 1.Standards and the problem of data integration Example: PSICQUIC and the PSICQUIC game 2.Introduction to ontologies. Exploring the Gene Ontology -Coffee break- 3.Introduction to protein-protein interactions (PPIs) IntAct: the molecular interactions database at the EBI -Lunch break- 4.Introduction to pathways Reactome: a database of human biological pathways -Coffee break- 5.Network representation and analysis: strategies and limitations Network generation and analysis through Cytoscape and PSICQUIC

2. Introduction to protein-protein interactions (PPIs)

3. EMBL-EBI A couple of definitions… Protein-protein interactions (PPIs): physical and selective contacts that happen between pairs of proteins, in certain molecular regions and in a defined biological context. Interactome: the totality of PPIs that happen in a cell / in an organism / in a specific biological context... Protein-protein interaction network: Graphical representation of a group of PPIs in which proteins are represented as nodes and interactions as edges.

4. EMBL-EBI Why protein-protein interactions? 1.To predict a protein biological function “guilt by association” proteins with similar functions should cluster together 2.To improve characterization of protein complexes and pathways interaction networks work as a draft map that brings detail to biological processes and pathways Gene level DNARNA Protein level 1 protein = 1 function 1 protein = n functions = n networks! WRONG!

5. EMBL-EBI Guilt by association Histone methyltransferase Role in early development and hematopoiesis Proto-oncogene Transcription factor Cyclin-dependent kinase Role in transcription regulation Mediator of RNA polymerase transcription activity Role in transcription regulation Transcriptional modulator Transcription regulation dependent on kinases Receptor-activated transcription modulator Transcription modulation, signal transduction, activated by kinases. Role in inhibition of wound healing Putative oncoprotein Transcription activation Putative oncoprotein Involved in transcription regulation Cyclin Regulation of cyclin kinase, transcription regulation and cell cycle control Something to do with transcription and cell cycle control

6. EMBL-EBI Glaab et al., BMC Bioinformatics, PMID: 21144022. Characterization of protein complexes and pathways Hook, B. and Schagat, T. [Internet] 2011. Available from: www.promega.com/resources/articles/pu bhub/functional-proteomics-techniques- to-isolate-and-characterize-the-human- proteasome/ www.promega.com/resources/articles/pu bhub/functional-proteomics-techniques- to-isolate-and-characterize-the-human- proteasome/

7. EMBL-EBI Yeast-two hybrid (Y2H) High-throughput X-ray diffraction studies Low- throughput Tandem affinity purification+ mass spectrometry (TAP-MS) Protein-protein interaction detection methods No single method can accurately reproduce a true binary interaction observed under physiological conditions – every interaction detected experimentally is fundamentally artefactual.

8. EMBL-EBI Protein-protein interaction detection methods Braun et al., Nat Methods, 2008, PMID: 19060903.

9. EMBL-EBI Binary interactions – Two participants Co-localization – Two or more participants closely located N-ary ints. (associations) – Complex purification Functional / direct ints. – E. g. enzymatic interactions Types of protein-protein interactions

10. EMBL-EBI 10 Binary interactions

11. EMBL-EBI 11 Colocalization

12. EMBL-EBI N-ary interactions (association) Schleiff et al., Nat Rev Mol Cell Biol. 2011. PMID: 211396380

13. EMBL-EBI Direct / functional interactions Usually in vitro assays Participants IDs are known in advance (predetermined) Examples – enzymatic assays, SPR, crystallography, methods using purified protein… Images from Wikipedia: http://en.wikipedia.org/wiki/X-ray_crystallography http://en.wikipedia.org/wiki/Surface_plasmon_resonance http://en.wikipedia.org/wiki/Protein_adsorption_in_the_food_industry

14. EMBL-EBI interaction domains Overlap in sequence ranges: Representing PPIs: interaction domains

15. EMBL-EBI Some experimental methods generate complex data: E. g. Tandem affinity purification (TAP) There are two algorithms to transform this information into binary data: Representing PPIs: The problem with complexes

16. EMBL-EBI De Las Rivas & Fontanillo, PLoS Computational biology, PMID: 20589078. Interactions databases: types

17. EMBL-EBI Databases: curation levels DEEP CURATION SHALLOW CURATION

18. EMBL-EBI Databases: curation levels Shallow curation BioGRID – active curation, limited number of model organisms HPRD – active curation, human focus, predicted interactions MPIDB – curation stopped, data re-located to IntAct, interactions in micro- organisms InnateDB – active curation, interactions related with innate immunity Deep curation IntAct – active curation, wide species coverage, all types of molecules MINT – active curation, wide species coverage, PPIs only DIP – active curation, wide species coverage, PPIs only MPACT – curation currently stopped, limited species coverage, PPIs only MatrixDB – active curation, extracellular matrix molecules only BIND – curation stopped in 2006/7, wide species coverage, all types of molecules – information getting outdated I2D – active curation, PPIs involved in cancer

19. EMBL-EBI Primary databases: coverage De Las Rivas & Fontanillo, PLoS Computational biology, PMID: 20589078. Human PPIs coverage in the main public primary databases (Dec 2009)

20. EMBL-EBI A standard for PPIs representation: the IMEx consortium www.imexconsortium.org Orchard et al., Nature Methods, PMID: 22453911.

21. IntAct: The molecular interactions database at the EBI

22. EMBL-EBI 1.Publicly available repository of molecular interactions (mainly PPIs) - >430K binary interactions taken from >12,000 publications (October 2013) 2.Data is standards-compliant and available via our website, for download at our ftp site or via PSICQUIC www.ebi.ac.uk/intact www.ebi.ac.uk/intact ftp://ftp.ebi.ac.uk/pub/databases/intact www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml 3.Provide open-access versions of the software to allow installation of local IntAct nodes. IntAct goals & achievements

23. EMBL-EBI Entry Publication Experiment 1 Interaction 1 Participant 1 Features Participant 2 Features Interaction 2 Experiment 2 Interaction 3Interaction 4 … … … [A] Publication level (entry) [B] Experiment level [C] Interaction level [D] Participant level [E] Feature level IntAct: Data storage schema

24. EMBL-EBI UniProt Knowledge Base www.uniprot.org Interactions can be mapped to the canonical sequence…... to splice variants...... or to post- processed chains

25. EMBL-EBI IntAct: PSI-MI ontology

26. EMBL-EBI “Lifecycle of an Interaction” Publication (full text) Sanity Checks (nightly) IntAct Curation pipeline CVs curator report Curation manual. reject Super curator annotate p1 p2 I exp IMEx MatrixDB Mint DIP Public web site FTP site accept check

27. EMBL-EBI CURATION DIRECT SUBMISSIONS PUBLISHED MOLECULAR INTERACTIONS DATA LARGE DATASETS FROM HIGH-THROUGHPUT PROJECTS IntAct: the role of the curator

28. EMBL-EBI CROSS-REFERENCES FAMILIES AND DOMAINS InterPro SMALL MOLECULES ChEBI FUNCTION Gene Ontology GENOME SEQUENCES Ensembl UniProtKB PROTEIN SEQUENCES LARGE DATASETS FROM HIGH-THROUGHPUT PROJECTS PUBLISHED MOLECULAR INTERACTIONS DATA CURATION DIRECT SUBMISSION Others STRUCTURES, ORGANISM, TISSUE...

29. EMBL-EBI Common curation platform Specific Data Dissemination Platforms General curation, large scale General curation, domain int. UniProt entry related Extracellular matrix Model organisms Immune system Commercial curation Cellular mechanics Regulatory interactions Specific curation focus/expertise Other DBs Host – pathogen interactions Cardiovascular proteins IntAct as a common curation platform

30. EMBL-EBI IntAct – Home Page www.ebi.ac.uk/intact

31. EMBL-EBI IntAct webpage-based search

32. EMBL-EBI IntAct webpage-based search Details of interaction Choice of UniProtKB or Dasty View

33. EMBL-EBI IntAct: changing the layout

34. EMBL-EBI IntAct: download formats

35. EMBL-EBI MITAB 2.7 specific columns (+27): Expansion method(s) Biological role(s) of interactors Experimental role(s) of interactors Type(s) of interactors Properties (CrossReference) of interactors / interaction Annotation(s) of interactors / interaction HostOrganism(s) Parameters of interaction Creation and update dates Checksum(s) of interactors / interaction Negative Feature(s) interactors Stoichiometry(s) interactors Participant(s) identification method(s) MITAB 2.5 Standard columns (15): ID(s) interactor A & B Alt. ID(s) interactor A & B Alias(es) interactor A & B Interaction detection method(s) Publication 1st author(s) Publication Identifier(s) Taxid interactor A & B Interaction type(s) Source database(s) Interaction identifier(s) Confidence value(s) PSIMITAB Columns

36. EMBL-EBI Interaction detail in IntAct

37. EMBL-EBI Detailed participant information: Dasty view

38. EMBL-EBI IntAct: filtering results

39. EMBL-EBI IntAct: visualizing results as a network

40. EMBL-EBI IntAct: using lists

41. EMBL-EBI IntAct: browse menu

42. EMBL-EBI IntAct: advanced search...

43. EMBL-EBI IntAct: MIQL syntax search

44. EMBL-EBI Searching and visualizing

45. EMBL-EBI Using lists

46. EMBL-EBI Checking details

47. EMBL-EBI Advanced search

48. EMBL-EBI Advanced search: using MIQL

49. EMBL-EBI Ontology search

50. EMBL-EBI Link to other PSICQUIC services

51. EMBL-EBI www.ebi.ac.uk/training/online/course/intact-molecular-interactions-ebi More about IntAct: “on-line” EBI courses

52. The PSICQUIC client: A unified gate to interactomics data

53. EMBL-EBI Unified query client: PSICQUIC www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml PSICQUIC Query MIQL input Interactions PSI-MI output PSICQUIC Registry PSICQUIC Service A PSICQUIC Service B PSICQUIC Service C

54. EMBL-EBI www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml Unified query client interface: PSICQUIC view

55. EMBL-EBI Acknowledgements Henning Hermjakob Group leader Rafael Jiménez Marine Dumousseau Noemí del Toro Developing team Sandra Orchard Margaret Duesbury Birgit Meldal Curation teamCoordinator