Cytoscape


 Stewart MacArthur
       2010
What is Cytoscape?
"Cytoscape is an open source
bioinformatics software platform for
visualizing molecular interaction
net...
Core Functions


      Network Visualization

 A   interacts   B
 B   interacts   C
 B   interacts   D
 B   interacts   E
...
Core Functions

Supports standard network and annotation file formats:
    SIF - Simple Interaction Format
    GML - Graph...
Core Functions
Search - Search nodes and edges with quick search or complex
          queries

Filter - Filter data based ...
Layouts
VizMapper
Plugins

Cytoscape's core functionality is extended by plugins

   Data retrieval from databases
      Agilent Literature ...
Data Retrieval: as a client for external
databases

       Protein Interaction database from EMBL-EBI

           Protein ...
Data Analysis: BiNGO
Biological Network Gene Ontology
Maere, S., Heymans, K. and Kuiper, M. (2005)
  BiNGO: a Cytoscape pl...
BiNGO
Biological Network Gene Ontology
Plugin: BiNGO
Biological Network Gene Ontology
Plugin: VistaClara

A visualization plugin for exploratory analysis of multi-
experiment microarray studies
Merge Networks
Network Analysis Plugins

MCODE - Finds clusters (highly interconnected regions) in a
network.

jActiveModules - Finds clu...
MCODE
An automated method for finding
molecular complexes in large protein
interaction networks.
Bader GD, Hogue CW. BMC
B...
jActiveModules

 finds active subnetworks
     clusters with significant changes in expression over
     subsets of condit...
References

Integration of biological networks and gene expression data using
Cytoscape
Cline et. al. Nature Protocols 2, ...
Practical
Case Study



Macrophages Stimulated with LPS
Expression arrays - time course
Clustering revealed group of early
coexpress...
Further Information


  Cytoscape.org
  Cytoscape Wiki
     User Manual
     Tutorials
  Bioinformatics Core Wiki - Tutori...
Network Analyser

Computing topological parameters of biological networks.
Assenov, Y et. al . Bioinformatics , 24(2):282-...
Plugin API and Scripting

 API and tutorials for plugin development in Java
 Scripting support for Python,Ruby, Javascript...
Other Plugins
  GenePro       Cerebral

  Cerebral
Plugin: Agilent Literature Search
Data Retrieval Plugin: Agilent Literature
Search
Meta-search Tool
 Automatic query of text based search engines
 e.g. PubM...
Cytoscape Talk 2010
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Cytoscape Talk 2010

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Introduction to Cytoscape talk given in March 2010 at the CRUK CRI. Cambridge UK.

It was design to give a broad introduction the features available in Cytoscape for wet lab researchers.

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Cytoscape Talk 2010

  1. 1. Cytoscape Stewart MacArthur 2010
  2. 2. What is Cytoscape? "Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data." Visualization tool for network data Free & open source Cross-Platform - Java Additional features available via Plugins Large development community Current Version 2.6.3 Original reference cited 1323 times (since 2003)
  3. 3. Core Functions Network Visualization A interacts B B interacts C B interacts D B interacts E C interacts B D interacts D
  4. 4. Core Functions Supports standard network and annotation file formats: SIF - Simple Interaction Format GML - Graph Modelling Language XGMML -eXtensible Graph Markup and Modeling Language BioPAX - Biological Pathway Exchange PSI-MI - Proteomics Standards Initiative - Molecular Interaction SBML - Systems Biology Markup Language OBO - Open Biomedical Ontologies .. .. Also Any delimited file (tab, comma etc) Excel
  5. 5. Core Functions Search - Search nodes and edges with quick search or complex queries Filter - Filter data based on any current data, number of interactions, shared nodes, expression level etc. Layout - Display networks in 2D with a variety of algorithms VizMapper - Customise display with colour mapping, e.g node colour to fold change or p-value, Edge width to significance etc.
  6. 6. Layouts
  7. 7. VizMapper
  8. 8. Plugins Cytoscape's core functionality is extended by plugins Data retrieval from databases Agilent Literature Search NCBI Pathway Commons IntACT BioNet Builder Data analysis BiNGO ClueGO VistaClara MCODE
  9. 9. Data Retrieval: as a client for external databases Protein Interaction database from EMBL-EBI Protein Interactions from Entrez Gene Collection of databases Data management system, e.g. annotation External datbases can be searched by gene or gene list, and results from multiple databases merged.
  10. 10. Data Analysis: BiNGO Biological Network Gene Ontology Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449. PubMed
  11. 11. BiNGO Biological Network Gene Ontology
  12. 12. Plugin: BiNGO Biological Network Gene Ontology
  13. 13. Plugin: VistaClara A visualization plugin for exploratory analysis of multi- experiment microarray studies
  14. 14. Merge Networks
  15. 15. Network Analysis Plugins MCODE - Finds clusters (highly interconnected regions) in a network. jActiveModules - Finds clusters with unexpectedly high levels of differential expression and correlated expression patterns across multiple conditions Network Analyser - Computes specific parameters describing the network topology, such as centralization, average number of neighbors and Heterogeneity etc.
  16. 16. MCODE An automated method for finding molecular complexes in large protein interaction networks. Bader GD, Hogue CW. BMC Bioinformatics . 2003 Jan 13;4(1):2. Finds clusters, highly interconnected regions, in networks Depending on context these could be: protein complexes sub-networks high-evidence interactions
  17. 17. jActiveModules finds active subnetworks clusters with significant changes in expression over subsets of conditions
  18. 18. References Integration of biological networks and gene expression data using Cytoscape Cline et. al. Nature Protocols 2, - 2366 - 2382 (2007) Cytoscape: a software environment for integrated models of biomolecular interaction networks Shannon et. al. Genome Research 13(11):2498-504. (2003) Exploring biological networks with Cytoscape software. Curr Protoc Bioinformatics. 2008 Sep;Chapter 8:Unit 8.13.
  19. 19. Practical
  20. 20. Case Study Macrophages Stimulated with LPS Expression arrays - time course Clustering revealed group of early coexpressed transcription factors (cluster 6) Motif Finding - ATF3 binding sites in promoters ATF3 Network showed interactions with NF-KB complex (light green) Motif Finding - ATF3 and NF-KB sites in cluster2 (expressed later) Cytokines IL6 and IL12b enriched for sites near promoter LPS -> ATF3 -> Cytokines, Previously unknown interactions
  21. 21. Further Information Cytoscape.org Cytoscape Wiki User Manual Tutorials Bioinformatics Core Wiki - Tutorial
  22. 22. Network Analyser Computing topological parameters of biological networks. Assenov, Y et. al . Bioinformatics , 24(2):282-284, 2008 analysis of biological networks calculates network topology parameters diameter of a network average number of neighbors number of connected pairs of nodes distributions of network parameters node degrees average clustering coefficients topological coefficients shortest path lengths
  23. 23. Plugin API and Scripting API and tutorials for plugin development in Java Scripting support for Python,Ruby, Javascript and Groovy Scripting can: add new functions automate analysis link new data sources export information test algorithms before creating plugin
  24. 24. Other Plugins GenePro Cerebral Cerebral
  25. 25. Plugin: Agilent Literature Search
  26. 26. Data Retrieval Plugin: Agilent Literature Search Meta-search Tool Automatic query of text based search engines e.g. PubMed, OMIM, USPTO

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