EMBL-EBI Workshop: Transcriptomics Data and Tools


  Friday 17 May 2019


University of Cambridge - Downing Site, Cambridge,  CB2 3AR, United Kingdom

Application opens: 

Tuesday 05 March 2019

Application deadline: 

Friday 17 May 2019


First come, first served


Charlotte Pearton

Registration fee: 

Free for Uni. Cambridge students and staff, see "How to apply" for more details

Registration closed

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Course Overview

This workshop will provide participants with an introduction to functional genomics resources at EMBL-EBI. It will cover how to access, retrieve and use the data from ArrayExpress. The second half focusses on Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. The workshop will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".


The module is suitable for researchers interested in gene expression analysis and visualisation. Those who are graduate students, postdocs and staff members from the University of Cambridge, affiliated institutions and other external Institutions or individuals, are invited to apply. No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.



  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions

Learning outcomes

After this course you should be able to:

  • Browse and retrieve functional genomics data from ArrayExpress with ease
  • Search and extract functional genomics data effectively with specific filter
  • Describe the caveats and limitations behind the searches made against the ArrayExpress database
  • Find information on the abundance and localisation of RNA (and proteins) in different species and biological conditions
  • Interpret gene expression analysis results through heatmap visualisation


Friday 17 May 2019
09:30-09:45 Welcome and introduction to EMBL-EBI resources and tools Nancy George / Silvie Fexova
09:45-10:45 Data quality: standards and ontologies Nancy George / Silvie Fexova
10:45-11:00 Tea/Coffee break
11:00-12:00 Discover functional genomics data with ArrayExpress Nancy George / Silvie Fexova
12:00-13:00 Lunch (not provided)
13:00-14:00 Discover functional genomics data with ArrayExpress: Practical session Nancy George / Silvie Fexova
14:00-15:00 Explore gene expression data with Expression Atlas Nancy George / Silvie Fexova
15:00-15:30 Tea/Coffee break
15:30-16:30 Explore gene expression data with Expression Atlas: Practical session Nancy George / Silvie Fexova
16:30-17:15 Single Cell Expression Atlas: a new tool for single cell transcriptomics Nancy George / Silvie Fexova
17:15-17:30 Course wrap-up and feedback Nancy George / Silvie Fexova