EMBL-EBI Bioinformatics resources for exploring functional genomics data

Date:

 Thursday 9 Friday 10 November 2017

Venue: 

Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120,  Heidelberg, Germany

Participation: 

By invitation

Contact: 

Monika Kulka

Registration closed

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Course Overview

This course will provide participants with an introduction to functional genomics resources at EMBL-EBI, in particular to ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas.

The course will focus on accessing data relevant to their areas of interests and on visualizing gene expression analysis results with Expression Atlas. It will also explain how to submit functional genomics data (e.g. microarray expression profiling, RNA-seq, ChIP-seq) to a public repository such as ArrayExpress and the importance of data standards for functional genomics.

Activities will include interactive presentations by the trainer and practical exercises to give the trainees hands on experiences.

Audience

This course is for wet-lab researchers at any career stage at the German Cancer research Centre, Heidelberg, interested in exploring functional genomic data and applying EMBL-EBI resources in their research.

No prior knowledge of programming is required, however an undergraduate level knowledge of biology and/or biochemistry is essential.

Modules and resources

Learning outcomes

After this course you should be able to:

  • Submit data to ArrayExpress through Annotare, and search for data of interest effectively.
  • Relate microarrays and RNA-seq data analysis in Expression Atlas to your work
  • Use Expression Atlas to answer expression related questions on genes and proteins of interest.

Programme

 

Time

Topic

Day 1 – Thursday 9th November 2017

09:30 - 10:00

Welcome and Introduction to EMBL-EBI resources

10:00 – 11:00

Data quality: standards, curation and ontologies

11:00 – 11:30

Tea/coffee break

11:30 - 12:30

Discover functional genomics data with ArrayExpress

12:30 - 13:30

Lunch

13:30 – 15:00

Practical session: ArrayExpress

15:00 – 15:30

Tea/coffee break

15:30 - 16:30

Annotare: ‘your’ web-form submission tool

16:30 - 17:30

Hands-on session: data submission with Annotare

17:30

End of Day 1

Day 2 – Friday 10th November 2017

09:00-10:30

Expression Atlas: gene expression results across species and biological conditions

10:30-11:00

Tea/coffee break

11:00-12:30

Practical session I: Expression Atlas

12:30-13:30

Lunch

13:30-14:30

Expression Atlas behind the scenes

14:30-15:30

Practical session II: Expression Atlas

15:30-16:00

Expression Atlas data integrated in other resources: Open Targets

16:00-16:30

RNASeq-er API: accessing RNA-seq analysis results

16:30-17:00

Course wrap-up and feedback

17:30

End of course