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

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

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

Do we need/have genome browsers? YES NO

Annotation: making sense

Ensembl and friends

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

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 www.ensemblgenomes.org 8 8

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

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

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

Variation on the Browser

Ensembl Comparative Genomics Gene Trees Homologues Protein Families Whole Genome Alignments

Region Comparison Stickleback, cod, medaka

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 http://www.ensembl.org/info/docs/funcgen/regulation_sources.html http://www.ensembl.org/Homo_sapiens/Experiment/

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

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

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

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

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?

Exercises

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

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

Learn more and connect with us ? www.ensembl.org/info/website/tutorials/index.html www.youtube.com/user/EnsemblHelpdesk helpdesk@ensembl.org

Acknowledgements Funding European Commission Framework Programme 7 Updated November 2012