1. Protein interactions and Pathways Tutorial Wellcome trust summer school Jyoti Khadake

2. 1.Choose a protein Rad51/BRCA2 2.Find out the properties of protein from Uniprotkb 3.Intact search with the protein of interest Mitab(save results as text) Check the information available 4.View network in Intact 5.Perform above search in Psicquic 6.View network 7.Import network in Cytoscape 8.Show additional information as node and edge attributes 9.Import another network and compare Outline

3. 1. Find out about the protein Go to: www.uniprot.orgwww.uniprot.org Search for Rad51 – AC of the human swissprot protein. Find out the type of protein Isoform information Protein and pathway information Master headline

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5. 2. Search in IntAct Master headline Go to: www.ebi.ac.uk/intactwww.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) www.ebi.ac.uk/ontology-lookup Export MI-TAB Go to additional interactions – IMEx and Psicquic

6. 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

7. Additional links- IMEx Psicquic Master headline

8. 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 3. Cytoscape- load network

9. Additional links - cytoscape Master headline http://www.cytoscape.org/document ation_users.html http://chianti.ucsd.edu/cyto_web/pl ugins/http://chianti.ucsd.edu/cyto_web/pl ugins/ http://cytoscape.wodaklab.org/wiki/ Presentations