Biological networks:
topological analysis and visualization using Cytoscape sofwtare

ELIXIR-IT training session

Young Minds at Work

YMK2024

The study of the networks of protein-protein interactions within a cell, called “interactome”, provides information about the organization of the cell and allows us to identify proteins and signaling pathways that are disrupted or deregulated during a disease condition.  

In this course, through a practical example, we will use the open-source software Cytoscape and some of its apps to extract protein-protein interaction data, build the network, visualize and explore it in order to detect topological properties, find potential topological clusters and perform functional network enrichment analysis.

  
 
Aims of the workshop 
• To provide practical demonstrations of several freely available protein-protein interactions resources.
• To improve competences in protein-protein network analysis.
• To improve the knowledge of Cytoscape and its network analysis and gene enrichment analysis tools.
 
 
Resources and tools covered 
• IMEx resources
• STRING
• Cytoscape
• IntactApp
• MCODE
• ClueGo
 
 
Learning Outcomes 
At the end of this course, the participants will be able to:
 Identify and access public data resources and tools to study protein-protein interactions 
 Interpret the information given in different molecular interaction databases
 Represent networks using Cytoscape
 Perform network and functional analysis
 
 
Course prerequisites 
Participants don’t need to have bioinformatics skills and previous knowledge of the tools that will be presented at the course. Attendees may bring in their own datasets for analysis, although example datasets will be available
Programme

December 10th, 2024

Time

Learning Experience

Topic

09:00-10:00

Lecture

Introduction to Protein-Protein Interactions (PPIs) and Molecular Interaction Resources

10:00-10:30

Lecture

Brief introduction to network biology and Cytoscape

10:30-10:45

Break

10:45-13:00

Exercise

Building a molecular interaction network and analysing its topological features via Cytoscape 

Important Dates

 Deadline for applications (via the YMW registration form): 30th November 2024
• Chosen participants will be notified by: 3rd December 2024
• Course date: 10th December 2024

Venue

This is an online course

Fee

The course does not include a fee

Registration

The application for participating to the training course is closed.


Selection procedure

A maximum of 30 candidates will be selected on a first-come- first-served basis. Selected participants will be notified by 3rd December 2024.

 

Instructors

Prof. Luana Licata – University of Rome “Tor Vergata”, ELIXIR-IT, Italy

Organizers

Prof. Anna Marabotti, University of Salerno, ELIXIR-IT, Italy 
Luana Licata, University of Rome “Tor Vergata”, ELIXIR-IT, Italy

Helpers

Alessia Pinto, PhD student, University of Rome “Tor Vergata”, ELIXIR-IT, Italy
Francesco Gregoris, University of Padua, Italy

Contacts

For all kinds of queries, please contact the organiser Anna Marabotti at:  amarabotti@unisa.it or please write to elixir.ita.training@gmail.com