Functional interpretation of toxicogenomics data

Date: Tuesday, April 8, 2014 - Thursday, April 10, 2014
Venue:  EMBL-EBI, Cambridge, UK

Course Overview

This course is intended to give life scientists training on how to explore and use protein interaction bioinformatics resources. More specifically, it illustrates potential next steps for data exploration beyond genomic analysis for those with an interest in toxicogenomics. This course looks at the data repositories – including the diXa FP7 toxicogenomic data repository - resources and tools available, introducing the principles of biological network and pathway analysis.


This course is aimed at bench-based biologists who are interested in toxicogenomics, and are involved in or embarking upon protein interaction and/or pathway related projects. The course requires no prior knowledge of pathway analysis or computer programming skills.


During this course you will learn about:

  • The diXa toxicogenomic data warehouse and associated resources for expression and chemical data
  • Molecular interaction and pathway databases: IntAct, Reactome
  • Network analysis tools: Cytoscape and selected plug-ins (BINGO)


After this course you should be able to:

  • Browse, search and access toxicogenomic, protein interaction and network data stored in publicly available repositories
  • Use bioinformatics tools to analyse biological networks and pathways
  • Overlay expression data using appropriate identifiers to visualise biological networks and pathways


Day 1 - 8 April 2014

10:00 Registration & Coffee
10:30 Introduction to EMBL-EBI & diXa [Slides]
11:30 The diXa toxicogenomic data warehouse [Slides] [Quiz]
12:00 Small Molecule Data - ChEMBL [Slides]
13:00 Lunch  
14:00 Introduction to Array Express [Slides] [Exercises]
15:00 Tea/Coffee Break  
15:30 Expression Atlas
17:00 Close of Day  
18:30 Course Dinner  

Day 2 - 9 April 2014

Slides and tutorials day 2
Supplementary Material day 2

09:00 Introduction to Molecular Interactions
09:30 Accessing data from the IntAct Molecular Interaction Database
10:30 Tea/Coffee Break  
11:00 Introduction to network analysis & Cytoscape
12:30 Lunch  
13:30 From raw data to network analysis
15:00 Tea/Coffee Break  
15:30 From raw data to network analysis
17:00 Close of Day  

Day 3 - 10 April 2014

09:00 Pathway based analysis (Reactome) [Slides] [Tutorial]
10:30 Tea/Coffee Break  
11:00 Pathway based analysis
12:30 Lunch  
13:30 From protein networks to mechanistic and predictive models
14:30 Course feedback
15:00 Close of Course


Please note that the registration fee of £100 includes:

  • Course materials 

  • Use of a computer in the EMBL-EBI IT Training Room throughout the course
  • Course dinner on Tuesday 8 April 2014

There will be a maximum of 30 participants on this course and registration is on a first-come, first-served basis.

The registration fee of £100 will need to be paid by credit/debit card at the time of registering. Please note that for members of the EMBL-EBI Industry Programme the costs will be covered by the Industry Programme. 

One Nucleus members will recieve a 40% discount on this event. 

Registration is now closed