Protein interactions and Pathways

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Protein interactions and Pathways
Tutorial

• Wellcome trust summer school
• Jyoti Khadake

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Outline

• Choose a protein Rad51/BRCA2
• Find out the properties of protein from Uniprotkb
• Intact search with the protein of interest
• Mitab(save results as text)
• Check the information available
• View network in Intact
• Perform above search in Psicquic
• View network
• Import network in Cytoscape
• Show additional information as node and edge
  attributes
• Import another network and compare

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1. Find out about the protein

• Go to www.uniprot.org
• Search for Rad51 AC of the human swissprot
  protein.
• Find out the type of protein
• Isoform information
• Protein and pathway information

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2. Search in IntAct

• Go to www.ebi.ac.uk/intact
• Search for Rad51 or Brca2 (Q06609 or P51587) AC
  of the human swissprot protein.
• Explore the methods used at www.ebi.ac.uk/ontology
  -lookup molecular interactions(MI)
• Export MI-TAB
• Go to additional interactions IMEx and Psicquic
  

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• Cont....
• Make excel files one for basic network one for
  attributes can use single file as well.
• ACProtein1,ACProtein2,interactionType
• Interaction detection method, pubmed,expansion
  method

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Additional links- IMEx Psicquic
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3. Cytoscape- load network

• Load basic network
• Use the edge interactionType attribute to show
  interaction type
• Import additional attributes from file or from
  online databases
• Use the edge and node variations
• What else can be done

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Additional links - cytoscape

• http//www.cytoscape.org/documentation_users.html
• http//chianti.ucsd.edu/cyto_web/plugins/
• http//cytoscape.wodaklab.org/wiki/Presentations