1. Denise Carvalho-Silva Ensembl Outreach
Exploring Ensembl EMBL-EBI/Wellcome Trust Summer School in Bioinformatics
Denise Carvalho-Silva
Ensembl Outreach

2. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: tutorial and exercises
Take home messages

3. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: tutorial and exercises
Take home messages

4. Do we need/have genome browsers?
YES NO

5. Annotation: making sense

6. Ensembl and friends

7. Vertebrate genomes www.ensembl.org pre.ensembl.org >80 genomes*
D. melanogaster
C. elegans
S. cerevisae
pre.ensembl.org
Sheep, human, xenopus
*Release 80
May2015

8. Non-vertebrate genomes
Extends the use of Ensembl to other species
Wider taxonomic range (v27, >25K genomes*)
*Release 27
June 2015
x 53
x 39
x 408
x 133
x 24,913
No virus yet. Rice, arabidopsis, bacteria, worms 8 8

9. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: tutorial and exercises
Take home messages

10. Goal: Generate set of well-supported genes
Ensembl genes
Automatic
Manual
Goal: Generate set of well-supported genes 10

11. Ensembl Genetic Variation
Aims:
Collect, integrate and annotate all known variants
Provide tools for comparison to other genomic data
Provide a framework for access and to improve understanding

12. Variation on the Browser

13. Ensembl Comparative Genomics
Gene Trees
Homologues
Protein Families
Whole Genome Alignments

14. Region Comparison
Stickleback, cod, medaka

15. Ensembl Gene Regulation
Goal: Annotate the genome with features that may play a role in the transcriptional regulation of genes
Multiple data sources: collection and summary

16. Ensembl Regulation build
raw data  Ensembl pipeline  Ensembl annotation
CGCTT
GAACA
GAACA
CGCTT
ACGTC
ACGTC
ChIP-Seq DNase1-Seq

17. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: Tutorial and exercises
Take home messages

18. Ensembl tools and advanced features
Custom data display
e.g. BAM, VCF, BigWig, BED,GTF, Track hubs
Programmatic access

19. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: Tutorial and exercises
Take home messages

20. Tutorial Coffee intake is a worldwide phenomenon
with Finland at the top, and UK in 44o place.
Find the chromosome locations of variants associated with this phenotype
Which variant has got the most significant association?
How many transcripts have been annotated in the gene reported to be associated with this trait?
Which tissues show higher expression levels for this gene?
What is the location of the orthologous gene in sheep?

21. Exercises

22. Today: an one-hour slot
Genome browsers
Data in Ensembl
Genes
Genetic Variation
Comparative Genomics
Gene Regulation
The Ensembl Tools and advanced features
Hands-on: Tutorial and exercises
Take home messages

23. Ensembl: wealth of data, wealth of access
Oh Yes!
And it’s 100% free

24. Learn more and connect with us?

25. Acknowledgements Funding European Commission Framework Programme 7
Updated November 2012