Functional Interpretation of Toxicogenomic Data


 Tuesday 8 Thursday 10 April 2014


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application deadline: 

Friday 28 March 2014


First come, first served


Holly Foster

Registration fee: 


Registration closed


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.

Syllabus, tools and resources

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


Time Topic Trainer
Day 1 - 8 April 2014
10:00 Registration & Coffee  
10:30 Introduction to EMBL-EBI & diXa Vera Matser 
11:30 The diXa toxicogenomic data warehouse Vera Matser 
12:00 Small Molecule Data - ChEMBL Francis Atkinson 
13:00 Lunch  
14:00 Introduction to Array Express Amy Tang 
15:00 Tea/Coffee Break  
15:30 Expression Atlas Amy Tang 
17:00 Close of Day  
18:30 Course Dinner at The Red Lion, Hinxton  
Day 2 - 9 April 2014
09:00 Introduction to Molecular Interactions Pablo Porras
09:30 Accessing data from the IntAct Molecular Interaction Database Pablo Porras
10:30 Tea/Coffee Break  
11:00 Introduction to network analysis & Cytoscape Pablo Porras 
12:30 Lunch  
13:30 From raw data to network analysis Pablo Porras 
15:00 Tea/Coffee Break  
15:30 From raw data to network analysis Pablo Porras 
17:00 Close of Day  
Day 3 - 10 April 2014
09:00 Pathway based analysis (Reactome) Phani Garapati 
10:30 Tea/Coffee Break  
11:00 Pathway based analysis Phani Garapati 
12:30 Lunch  
13:30 From protein networks to mechanistic and predictive models Julio Saez-Rodriguez 
14:30 Course feedback Vera Matser 
15:00 Close of Course