5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI

Living cells contain crowded and diverse molecular environments Proteins constitute ~30% of E. coli and ~5% of yeast cytoplasm by weight ~2000 protein types are co-expressed co-localized in yeast cytoplasm

3 Example of a PPI Network Nodes – proteins Edges – interactions >80% of proteins are all connected in one giant cluster of PPI network

4 Why is it useful to study PPI networks? Proteins are the workhorses of cell, carrying out catalytic reactions, transport, forming viral caspids, transmitting information from DNA to RNA, traverse membranes, forming regulated channel, make possible synthesis of new proteins, responsible for degradation of unnecessary proteins, vehicles of immune response One way to predict protein function is through identification of binding partners – Guilt by Association If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation

5 Why is it useful to study the structure of PPI networks? Common properties of biological networks Can help us relate network structure to biological function Protein’s relative position in a network Correlate conserved functional modules with protein complexes

6 1.Publicly available repository of molecular interactions (mainly PPIs) - ~300K binary interactions taken from >5,300 publications (May 2012) 2.Data is standards-compliant and available via our website, for download at our ftp site or via PSICQUIC 3.Provide open-access versions of the software to allow installation of local IntAct nodes. IntAct goals & achievements ftp://ftp.ebi.ac.uk/pub/databases/intact

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

8 UniProt Knowledge Base Interactions can be mapped to the canonical sequence….. to splice variants.... or to post- processed chains

Relationship with UniProtKB Master headline Protein sequence Data filters Other IMEx databases High confidence PPIs In place Early 2012 Interaction curation Other DBs

10 Data model Support for detailed features i.e. definition of interacting interface Interacting domains Overlay of Ranges on sequence:

11 How to deal with Complexes Some experimental protocol do generate complex data: Eg. Tandem affinity purification (TAP) One may want to convert these complexes into sets of binary interactions, 2 algorithms are available:

12 PSI-MI Data format Data distribution Control vocabulary Data submission Standard format Tools PSICQUIC PSI-MI CV Reporting guideline MIMIx Tools PSI-MI XML PSI-MITAB XML Java API MITAB Java API XMLMakerFlattener Semantic Validator RPsiXML (Bioconductor) PSI-MI XML files PSI Excel Sheet PSI Web Form Servers Registry Clients PSISCORE Servers Registry Clients

EBI is an Outstation of the European Molecular Biology Laboratory. Performing and visualing a Simple Search EBI Walthrough May 2009 EBI Data, Standards and Tools

14 IntAct – Home Page

Performing a Simple Search 15

16 Visualizing - networkView From search to networkView…

Extend and Visualise your Search 17

18 Visualizing - networkView

Cytoscape Web Cytoscape Web - web-based network visualization tool Modeled after Cytoscape – open-source, interactive, customizable and easily integrated into web sites. Contains none of the plugin architecture functionality of Cytoscape 19

Master headline Visualization Opening the network in Cytoscape…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Cytoscape Plugins 27

EBI is an Outstation of the European Molecular Biology Laboratory. Exploring a single interaction in more depth

Interaction detail 29 First search from the home page… Choice of UniProtKB or Dasty View Details of interaction

Detail of interaction 30 UniProt Taxonomy PubMed Expansion method Details of interaction

Changing the tabular view 31

Participant information 32 Search result for ‘RAD1’

Interaction detail 33 First search from the home page… Details of interaction

34 Viewing Interaction Details Additional information

Interaction Details 35

IntAct – Home Page-Quick Search 36

Advanced search: Fields Filtering options Add more filtering options

38 Searching with MIQL First search from the home page… Using the Molecular Interaction Query Language (MIQL), one can also build complex queries List of terms one can query on :

39 Browsing – Molecule View Binary view of o60671_human

40 Browsing – extending your search

41 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

EBI is an Outstation of the European Molecular Biology Laboratory. Performing and visualing a Simple Search EBI Walthrough May 2009 EBI Data, Standards and Tools

43 IntAct – Home Page

Performing a Simple Search 44

45 Visualizing - networkView From search to networkView…

Extend and Visualise your Search 46

47 Visualizing - networkView

Cytoscape Web Cytoscape Web - web-based network visualization tool Modeled after Cytoscape – open-source, interactive, customizable and easily integrated into web sites. Contains none of the plugin architecture functionality of Cytoscape 48

Master headline Visualization Opening the network in Cytoscape…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Applying a better graph layout…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Master headline Visualization Highlighting network properties…

Cytoscape Plugins 56

EBI is an Outstation of the European Molecular Biology Laboratory. Exploring a single interaction in more depth

Interaction detail 58 First search from the home page… Choice of UniProtKB or Dasty View Details of interaction UniProt Taxonomy PubMed/IMEx ID

Detail of interaction 59 Expansion method Details of interaction Interaction Score

Interaction Score All evidences of Protein A interacting with Protein B are clustered. Evidences are scored according to a. Interaction detection method b. Interaction type c. Number of publications interaction has been observed in Score is normalised on 0-1 scale Low score – low confidence interaction High score – high confidence interaction 60

Changing the tabular view 61

Participant information 62 Search result for ‘RAD1’

Interaction detail 63 First search from the home page… Details of interaction

64 Viewing Interaction Details Additional information

Interaction Details 65

IntAct – Home Page-Quick Search 66

Advanced search Filtering options Add more filtering options

Ontology search 68

69 Searching with MIQL First search from the home page… Using the Molecular Interaction Query Language (MIQL), one can also build complex queries List of terms one can query on :

70 Browsing – Molecule View Binary view of o60671_human

71 Browsing – extending your search

72 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?