Introduction presentation

You can download the presentation from here.


Quiz


As a start of the hands-on session, we prepared a short quiz. You can work alone or in a group (up to 4 people).
After the quiz there will be a coffee break before we start with the tutorial at 11:00.

We have a Winner !

Team “Stathis”

Congratulations!!!

Prize will be handed out at the end of the lecture 🙂


Tutorial

In this tutorial you are going to perform network analysis in Cytoscape to help biological interpretation. You are going to:

  • Browse Protein-protein interactions in STRING.
  • Extend a biological pathway with regulatory interactions
  • Find interaction data and visualize your data on the network

Below you can find some background information about the STRING database, Cytoscape and few of its plugins (GPML plugin, MIMI plugin and Cytargetlinker plugin) to be used in the hands-on session.


Background Information

STRING

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations derived from Genomic Context, High-throughput Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently covers 5’214’234 proteins from 1133 organisms.

Cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.

Cytoscape Apps plugins

Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.

GPML plugin

The GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format. This plugin makes it possible open and save GPML pathways from Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. See here for more information.

MiMI plugin

The MiMI plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching. See here for more information.

Cytargetlinker plugin

The CyTargetLinker plugin extends biological networks with regulatory interactions, for example miRNA-target gene information. Network nodes need to have an attribute containing a biological identifier, eg. NCBI Gene, to link to regulatory information. It is also necessary to download regulatory interaction networks (RINs, available from the website) or create your own. See here for more information.