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BiNoM Tutorial

BiNoM Tutorial. Andrei Zinovyev, Laurence Calzone UMR U900 INSERM/Institut Curie/Ecole des Mines de Paris Wednesday, April 30th. BiNoM is a plugin for Cytoscape. http://cytoscape.org/. Install and Start Cytoscape+BiNoM.

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BiNoM Tutorial

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  1. BiNoM Tutorial Andrei Zinovyev, Laurence Calzone UMR U900 INSERM/Institut Curie/Ecole des Mines de Paris Wednesday, April 30th

  2. BiNoM is a plugin for Cytoscape http://cytoscape.org/

  3. Install and Start Cytoscape+BiNoM 1) Download Cytoscape installer version 2.4.0 from http://cytoscape.org 2) Download BiNoM from http://bioinfo-out.curie.fr/projects/binom/BiNoM_all.jar 3) Copy BiNoM_all.jar into the ‘plugins’ folder of Cytoscape 4) Remove (better, backup) xercesImpl.jar from the ‘lib’ folder of Cytoscape Attention : BiNoM is not yet compatible with the latest version of Cytoscape 2.6.0. These technical issues will be resolved very soon.

  4. Starting course about Cytoscape

  5. Short introduction into Cytoscape

  6. Short introduction into Cytoscape Selected nodes

  7. Short introduction into Cytoscape

  8. BiNoM – Biological Network Manager

  9. Naming convension

  10. Section 1. Basic Network Analysis tools in BiNoM

  11. Importing CellDesigner (SBML) files Open NFKB_final.xml example

  12. Importing CellDesigner (SBML) files Reaction network

  13. Choose in the menuPlugins / BiNoM Analysis / Prune graph Result of operation Initial network

  14. Choose in the menuPlugins / BiNoM Analysis / Monomolecular reactions to edges Result of operation Initial network

  15. Choose in the menuPlugins / BiNoM Analysis / Exclude intermediate nodes Initial network Result of operation

  16. Choose in the menuPlugins / BiNoM Analysis / Material components NFkB Initial network IkB

  17. 1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis

  18. 1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis

  19. Section 2. BiNoM and BioPAX

  20. Biological PAthway eXchange format Database Exchange Formats SimulationModel Exchange Formats BioPAX Small Molecules (CML) SBML, CellML PSI Molecular Interactions Pro:Pro All:All Genetic Interactions Biochemical Reactions Metabolic Pathways Low Detail High Detail Rate Formulas Interaction Networks Molecular Non-molecular Pro:Pro TF:Gene Genetic Regulatory Pathways Low Detail High Detail

  21. BioPAXis formulated on Web Ontology Language (OWL) BioPAX level 2.0

  22. Importing BioPAX files Open example file at Desktop/ Pathway Charting/ MAPK_Reactome.owl

  23. Reaction network (RN) Apply Layout -> yFiles -> Organic layout

  24. Pathway hierachy (PS) Apply Layout -> yFiles -> Hierarchic layout

  25. Protein-protein interactions (PP) Apply Layout -> yFiles -> Organic layout

  26. Example of combined view Apply Plugins->Merge networks

  27. Alternative Pathway viewReimport the MAPK_Reactome example with new pathway hierarchy options

  28. Get BioPAX annotationPlugins / BiNoM BioPAX Utils/BioPAX Property Editor Select some Nodes first

  29. Get BioPAX annotationBiNoM BioPAX Utils/BioPAX Property Editor Browse by clicking at the color labels

  30. Get Complete BioPAX annotationPlugins / BiNoM BioPAX Utils / BioPAX Class tree…

  31. Exporting subnetwork: 1.Select subtree 2.File->New->Network->From selected nodes, all edges

  32. Exporting subnetwork: 3. Plugins->BiNoM->Export current network to BioPAX4. Associate with MAPK_Reactome5. Save to ERK2.owl

  33. Exporting subnetwork: 6. Reopen ERK2.owl using Plugin->BiNoM I/O-> Import BioPAX

  34. Section 3. Using BiNoM with pathway databases

  35. Pathway Database -> BioPAX -> BiNoM query Reactome Cancer Cell Map Big BioPAX file INOH BiNoM Nature/NCI Pathway Interaction HumanCyc KEGG BioBase

  36. To work with big BioPAX file, BiNoM user should generate BioPAX index Reactome Index .xgmml file Query Reactome .owl file BiNoM BiNoM Network

  37. Preparing database: Plugins / BiNoM BioPAX Query / Generate Index

  38. Loading index:Plugins / BiNoM BioPAX Query / Load Index The accession number file (list of synonyms) is optional. It facilitates identifying proteins by name or other Ids

  39. Plugins / BiNoM BioPAX Query -> Select entities IGF_1 IGFBP_3 pRB

  40. Plugins / BiNoM BioPAX Query / Standard query

  41. Get all reactions in which IGF_1 is involvedPlugins / BiNoM BioPAX Query / Standard query

  42. Extract all selected reaction annotationsPlugins / BiNoM BioPAX Query / Standard query

  43. Plugins / BiNoM Analysis / Extract Reaction Network Simplifying the query result view Plugins / BiNoM Analysis / Mono-molecular Reactions To Edges

  44. Finding the shortest path from one protein to another Plugins / BiNoM BioPAX Query / Index Path Analysis

  45. Finding the shortest path and suboptimal path from one protein to another Plugins / BiNoM BioPAX Query / Index Path Analysis 1) Select nodes 2) Open dialog, change parameters 3) Apply hierarchic layout

  46. Q: Why are there some hanging nodes in the tree? A: Because there are connections “through complexes”

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