BiNoM Tutorial

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BiNoM Tutorial

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

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BiNoM is a plugin for Cytoscape
http//cytoscape.org/
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Install and Start CytoscapeBiNoM

• 1) Download Cytoscape installer version 2.4.0
  from http//cytoscape.org
• 2) Download BiNoM from
• http//bioinfo-out.curie.fr/projects/binom/BiNoM_a
  ll.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.

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Starting course about Cytoscape
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Short introduction into Cytoscape
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Short introduction into Cytoscape
Main concept directed graph with attributes
AttributeYName Value
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Short introduction into Cytoscape
Selected nodes
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Short introduction into Cytoscape
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BiNoM Biological Network Manager
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Naming convension
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Section 1. Basic Network Analysis tools in BiNoM
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Importing CellDesigner (SBML) files
Open NFKB_final.xml example
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Importing CellDesigner (SBML) files
Reaction network
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Choose in the menuPlugins / BiNoM Analysis /
Prune graph
Result of operation
Initial network
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Choose in the menuPlugins / BiNoM Analysis /
Monomolecular reactions to edges
Result of operation
Initial network
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Choose in the menu Plugins / BiNoM Analysis /
Exclude intermediate nodes
Initial network
Result of operation
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Choose in the menu Plugins / BiNoM Analysis /
Material components
NFkB
Initial network
IkB
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BiNoM Analysis / Get cycle decomposition
Apply from the initial network
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1. Select NFkB_at_nucleus and IkB_alphaNFkB nodes
(holding Shift key)2. Choose in the menu
Plugins / BiNoM Analysis / Path analysis
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1. Select NFkB_at_nucleus and IkB_alphaNFkB nodes
(holding Shift key)2. Choose in the menu
Plugins / BiNoM Analysis / Path analysis
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BiNoM I/O Export current network to CellDesigner

1. Select some nodes
2. File-gtNew-gtNetwork-gtFrom selected nodes, all
   edges
3. BiNoM I/O-gtExport current network to CellDesigner
4. Associate the network with NFKB_final.xml
5. Save to a new xml file
6. Open the newly created file in CellDesigner

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Section 2. BiNoM and BioPAX
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Biological PAthway eXchange format
Database Exchange Formats
Simulation Model Exchange Formats
BioPAX
Small Molecules (CML)
SBML, CellML
PSI
Molecular Interactions ProPro
AllAll
Biochemical Reactions
Genetic Interactions
Metabolic Pathways Low Detail High
Detail
Rate Formulas
Interaction Networks Molecular
Non-molecular ProPro TFGene
Genetic
Regulatory Pathways Low Detail High
Detail
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BioPAXis formulated on Web Ontology Language
(OWL)
BioPAX level 2.0
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Importing BioPAX files
Open example file at Desktop/ Pathway
Charting/ MAPK_Reactome.owl
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Reaction network (RN)
Apply Layout -gt yFiles -gt Organic layout
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Pathway hierachy (PS)
Apply Layout -gt yFiles -gt Hierarchic layout
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Protein-protein interactions (PP)
Apply Layout -gt yFiles -gt Organic layout
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Example of combined view
Apply Plugins-gtMerge networks
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Alternative Pathway viewReimport the
MAPK_Reactome example with new pathway hierarchy
options
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Get BioPAX annotationPlugins / BiNoM BioPAX
Utils/BioPAX Property Editor
Select some Nodes first
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Get BioPAX annotationBiNoM BioPAX Utils/BioPAX
Property Editor
Browse by clicking at the color labels
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Get Complete BioPAX annotationPlugins / BiNoM
BioPAX Utils / BioPAX Class tree
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Exporting subnetwork 1.Select subtree
2.File-gtNew-gtNetwork-gtFrom selected nodes, all
edges
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Exporting subnetwork 3. Plugins-gtBiNoM-gtExport
current network to BioPAX4. Associate with
MAPK_Reactome5. Save to ERK2.owl
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Exporting subnetwork 6. Reopen ERK2.owl using
Plugin-gtBiNoM I/O-gt Import BioPAX
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Section 3. Using BiNoM with pathway databases
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Pathway Database -gt BioPAX -gt BiNoM query
Reactome
Cancer Cell Map
Big BioPAX file
INOH
BiNoM
Nature/NCI Pathway Interaction
HumanCyc
BioBase
KEGG
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To work with big BioPAX file, BiNoM user should
generate BioPAX index
Reactome Index .xgmml file
Query
Reactome .owl file
BiNoM
BiNoM
Network
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Preparing database Plugins / BiNoM BioPAX Query
/ Generate Index
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Loading indexPlugins / BiNoM BioPAX Query /
Load Index
The accession number file (list of synonyms) is
optional. It facilitates identifying proteins by
name or other Ids
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Plugins / BiNoM BioPAX Query -gt Select entities
IGF_1 IGFBP_3 pRB
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Plugins / BiNoM BioPAX Query / Standard query
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Get all reactions in which IGF_1 is
involvedPlugins / BiNoM BioPAX Query / Standard
query
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Extract all selected reaction annotationsPlugins
/ BiNoM BioPAX Query / Standard query
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Plugins / BiNoM Analysis / Extract Reaction
Network
Simplifying the query result view
Plugins / BiNoM Analysis / Mono-molecular
Reactions To Edges
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Finding the shortest path from one protein to
another Plugins / BiNoM BioPAX Query / Index Path
Analysis
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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
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Q Why are there some hanging nodes in the
tree? A Because there are connections through
complexes