Interaction network analysis serves an effective gateway into systems-level analysis, thanks in part to the abundance of publicly-available data and software methods. This tutorial emphasizes the following three aspects of interaction network analysis: what biological questions can be addressed, where the necessary data might be found, and how to perform the analysis and interpret the results. Network analysis is illustrated using the open-source software package Cytoscape. The course is lectured by Dr. Melissa Cline, Pasteur Institute, France.

The course consists of lectures and hands-on exercises. The lectures cover general backgound, while the exercises introduce Cytoscape and its different plugins. Links to the exercises and the lecture material (slides and videos) can be found below. The datasets used in the exercises can be downloaded here. The lecture videos can be viewed using RealPlayer.

Course program

1. Introduction and basic Cytoscape operation
- Introduction (slides, exercises, video)
- Biological network data, getting interactions from public databases (slides, exercises, video)

2. Advanced Cytoscape operation
- Literature search (slides, exercises, video)
- GO ontology (slides, exercises, video)

3. Cytoscape and mRNA expression
- Overlaying expression on the network (slides, exercises, video)
- Expression data interpretation using text mining and GO (slides, exercises, video)

4. Advanced concepts in network topology
- Network modules and complexes (slides, exercises, video)
- Domain interaction networks (slides, exercises, video)

For more information, please contact eija.korpelainen@csc.fi