Transcript BiNoM Tutorial Andrei Zinovyev, Laurence Calzone Wednesday, April 30th

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
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.
Starting course about Cytoscape
Short introduction into Cytoscape
Short introduction into Cytoscape
Selected nodes
Short introduction into Cytoscape
BiNoM – Biological Network Manager
Naming convension
Section 1. Basic Network Analysis
tools in BiNoM
Importing CellDesigner (SBML) files
Open NFKB_final.xml
example
Importing CellDesigner (SBML) files
Reaction network
Choose in the menu
Plugins / BiNoM Analysis / Prune graph
Initial network
Result of operation
Choose in the menu
Plugins / BiNoM Analysis / Monomolecular reactions to edges
Initial network
Result of operation
Choose in the menu
Plugins / BiNoM Analysis / Exclude intermediate nodes
Initial network
Result of operation
Choose in the menu
Plugins / BiNoM Analysis / Material components
NFkB
Initial network
IkB
1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)
2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis
1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)
2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis
Section 2. BiNoM and BioPAX
Biological PAthway eXchange format
Database
Exchange Formats
Simulation Model
Exchange Formats
BioPAX
Small
Molecules
(CML)
PSI
Molecular Interactions
Pro:Pro
All:All
SBML,
CellML
Genetic
Interactions
Metabolic
Low Detail
Biochemical
Reactions
Pathways
High Detail
Interaction Networks
Molecular
Pro:Pro
Non-molecular
TF:Gene
Genetic
Regulatory Pathways
Low Detail
High Detail
Rate
Formulas
BioPAX
is formulated on
Web Ontology
Language (OWL)
BioPAX level 2.0
Importing BioPAX files
Open example file
at
Desktop/
Pathway Charting/
MAPK_Reactome.owl
Reaction network (RN)
Apply Layout -> yFiles -> Organic layout
Pathway hierachy (PS)
Apply Layout -> yFiles -> Hierarchic layout
Protein-protein interactions (PP)
Apply Layout -> yFiles -> Organic layout
Example of combined view
Apply Plugins->Merge networks
Alternative Pathway view
Reimport the MAPK_Reactome example
with new pathway hierarchy options
Get BioPAX annotation
Plugins / BiNoM BioPAX Utils/BioPAX Property Editor
Select some
Nodes first
Get BioPAX annotation
BiNoM BioPAX Utils/BioPAX Property Editor
Browse by clicking at the color labels
Get Complete BioPAX annotation
Plugins / BiNoM BioPAX Utils / BioPAX Class tree…
Exporting subnetwork:
1.Select subtree
2.File->New->Network->From selected nodes, all edges
Exporting subnetwork:
3. Plugins->BiNoM->Export current network to BioPAX
4. Associate with MAPK_Reactome
5. Save to ERK2.owl
Exporting subnetwork:
6. Reopen ERK2.owl using Plugin->BiNoM I/O-> Import BioPAX
Section 3. Using BiNoM with
pathway databases
Pathway Database -> BioPAX -> BiNoM query
Reactome
Cancer
Cell Map
Big
BioPAX
file
INOH
Nature/NCI
Pathway Interaction
HumanCyc
KEGG
BioBase
BiNoM
To work with big BioPAX file,
BiNoM user should generate BioPAX index
Reactome
.owl file
BiNoM
Reactome
Index
.xgmml file
Query
BiNoM
Network
Preparing database:
Plugins / BiNoM BioPAX Query / Generate Index
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
Plugins / BiNoM BioPAX Query -> Select entities
IGF_1 IGFBP_3 pRB
Plugins / BiNoM BioPAX Query / Standard query
Get all reactions in which IGF_1 is involved
Plugins / BiNoM BioPAX Query / Standard query
Extract all selected reaction annotations
Plugins / BiNoM BioPAX Query / Standard query
Plugins / BiNoM Analysis / Extract Reaction Network
Simplifying the query result view
Plugins / BiNoM Analysis / Mono-molecular Reactions To Edges
Finding the shortest path from one protein to another
Plugins / BiNoM BioPAX Query / Index Path Analysis
Finding the shortest path and suboptimal path from one protein to another
Plugins / BiNoM BioPAX Query / Index Path Analysis
2) Open dialog, change parameters
1) Select nodes
3) Apply hierarchic layout
Q: Why are there some hanging nodes in the tree?
A: Because there are connections “through complexes”