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The IntAct Database

The IntAct Database. Sandra Orchard & Birgit Meldal. IntAct goals & achievements. Publicly available repository of molecular interactions (mainly PPIs) - > 333K binary interactions taken from > 6620 publications (Aug 2013)

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The IntAct Database

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  1. The IntAct Database Sandra Orchard & Birgit Meldal

  2. IntAct goals & achievements • Publicly available repository of molecular interactions (mainly PPIs) - >333K binary interactions taken from >6620 publications (Aug 2013) • Data is standards-compliant and available via our website, for download at our ftp site or via PSICQUIC • Provide open-access editor for those who wish to curate molecular interactions. http://www.ebi.ac.uk/intact ftp://ftp.ebi.ac.uk/pub/databases/intact www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml

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

  4. UniProt Knowledge Base Interactions can be mapped to the canonical sequence… .. to splice variants.. http://www.ebi.uniprot.org/ .. or to post-processed chains

  5. Master headline Relationship with UniProtKB Other IMEx databases Interaction curation Protein sequence Data filters Other DBs High confidence PPIs

  6. Interacting domains Overlay of Ranges on sequence: Data model • Support for detailed featuresi.e. definition of interacting interface

  7. 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:

  8. Performing and visualing a Simple Search

  9. IntAct – Home Page http://www.ebi.ac.uk/intact

  10. Performing a Simple Search

  11. Visualizing - networkView From search to networkView…

  12. Extend and Visualise your Search

  13. Visualisation – network view

  14. 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 Cytoscape Web

  15. Master headline Visualisation Opening the network in Cytoscape…

  16. Master headline Visualization Applying a better graph layout…

  17. Master headline Visualization Applying a better graph layout…

  18. Master headline Visualization Highlighting network properties…

  19. Master headline Visualization Highlighting network properties…

  20. Master headline Visualization Highlighting network properties…

  21. Master headline Visualization Highlighting network properties…

  22. Cytoscape Plugins

  23. Exploring a single interaction in more depth

  24. Interaction detail Choice of UniProtKB or Dasty View UniProt Details of interaction PubMed/IMEx ID

  25. Detail of interaction Expansion method Details of interaction Interaction Score

  26. 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 Interaction Score

  27. Participant information Search result for ‘RAD1’

  28. Browsing – Molecule View Binary view of o60671_human

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

  30. Viewing Interaction Details Additional information

  31. Interaction Details

  32. IntAct – Home Page-Quick Search

  33. Advanced search Filtering options Add more filtering options

  34. Ontology search

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

  36. Network analysis Analyzing protein-protein interaction networks. Koh GC , Porras P , Aranda B , Hermjakob H , Orchard SE PMID:22385417 J Proteome Res [2012 (11) ] page info:2014-31

  37. www.ebi.ac.uk/training/online

  38. ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

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