Building networks and pathways with Cytoscape

Introduction to networks, pathways and ID mapping

Trainer: Marton Olbei

Overview: This section introduces concepts in network biology and an overview of Cytoscape, a commonly used program for building networks and pathways.

Learning outcomes

By the end of this session you will be able to:

• Describe the concept in network biology
• Explore the applications of Cytoscape in building molecular networks

Materials:

• Presentation slides

Practical exercise with Cytoscape

Overview: In this session you can try an exercise with Cytoscape, a commonly used program in network biology. The main topics this session covers include how to import interaction information, what interaction resources are available for researchers, how to manipulate interaction data, how to map various identifiers to harmonise data coming from different resources, how to analyse and evaluate network information, how to integrate -omics data, and how to visualise it in tandem with various network characteristics. After the exercise you will be able to independently query interaction data, contextualise them using -omics information, and visualise them using Cytoscape.

Materials:

• Data integration with Cytoscape – practical
• Functional insight into biological data through network analysis
• File – multiomics_course_net.cys
• Table – GSE6731.top.table.tsv