1. Introduction to IntAct Pablo Porras Millán, IntAct pporras@ebi.ac.uk

2. Session outline Introduction to protein-protein interactions (PPIs) What are PPIs? Representing PPIs PPI databases IntAct: the molecular interactions database at the EBI Data structure and curation model Using the IntAct website

3. Introduction to protein-protein interactions (PPIs)

4. EMBL-EBI A definition… 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... Proteasome image from Hook, B. and Schagat, T. [Internet] 2011. Available from: www.promega.com/resources/articles/pubhub/functional-proteomics-techniques-to-isolate-and-characterize-the-human-proteasome/ www.promega.com/resources/articles/pubhub/functional-proteomics-techniques-to-isolate-and-characterize-the-human-proteasome/

5. 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!

6. 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.

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

8. 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

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

10. EMBL-EBI Primary databases: coverage and biases Roland et al., Cell, PMID: 25416956. De Las Rivas & Fontanillo, PLoS Computational biology, PMID: 20589078. Human PPIs coverage in the main public primary databases (Dec 2009) Popularity bias in publicly available databases (2013)

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

12. IntAct: The molecular interactions database at the EBI

13. EMBL-EBI 1.Publicly available repository of molecular interactions (mainly PPIs) - >530K binary interaction evidences taken from >13,800 publications (September 2015) 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

14. 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

15. EMBL-EBI IntAct: PSI-MI ontology

16. 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

17. 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... IntAct: the role of the curator

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

19. 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

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

21. EMBL-EBI IntAct webpage-based search

22. EMBL-EBI IntAct webpage-based search Details of interaction Link to external resource (UniProtKB) Details about controlled vocabulary term describing interaction detection method

23. EMBL-EBI IntAct: changing the layout

24. EMBL-EBI IntAct: download formats

25. 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

26. EMBL-EBI Interaction detail in IntAct

27. EMBL-EBI Interaction detail in IntAct

28. EMBL-EBI Interaction detail in IntAct

29. EMBL-EBI Interaction detail in IntAct

30. EMBL-EBI Filtering results

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

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

33. EMBL-EBI IntAct: browse menu

34. EMBL-EBI IntAct: Other searches

35. EMBL-EBI IntAct: Advanced search

36. EMBL-EBI IntAct: Advanced search

37. EMBL-EBI IntAct: Advanced search...

38. EMBL-EBI IntAct: MIQL syntax search

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

40. EMBL-EBI Acknowledgements Max Koch Developing team Sandra Orchard Curation team MI Team leader Margaret Duesbury Birgit Meldal Mariaestela Ortiz