1. Genome Browsers Carsten O. Daub Omics Science Center RIKEN, Japan May 2008

2. Outline Give some impression of the intuitive handling of the browsers Highlight some of the specific functions Point out some of the strengths of the different browsers

3. General comments We will focus on two genome growsers in this lecture UCSC genome browser ENSEMBL genome browser Some comments about the RIKEN FANTOM3 genome browser

4. General comments cont’d. The genome browsers are parts of bigger genome information resources Their main purpose is to graphically display complex information And to put this information into the genomic context We will not discuss all of the rich functionalities of UCSC and ENSEMBL here

5. General comments cont’d. Genome browsers are tools to –display various types of information –in the context of the genome

6. The context of the genome Graphical representation of the genome The chromosomes are displayed as straight ’strings’ With coordinates for the positions Various features are aliged to the chromosomes and displayed as tracks

7. What information is displayed? Which features can be displayed in such a way? Which features NOT?

8. UCSC genome browser

9. chr7

10. Mouseover effect

11. Zoom in

13. Tracks

14. Comments on Gene models Some comments on gene models: different databases have different ways to define gene models Common examples are NCBI: RefSeq, ’Known genes’ ENSEMBL: Known genes, Novel genes, Predicted genes What are the differences of the models? Which one is the better model?

15. stat3

18. Tracks in the Genome Browser Various types of information are aligned to the genome in groups, so calles tracks Each track contains a logical unit of information –Different gene models –Experimental evidence: cDNA, mRNA, EST –Expression and regulation –Repeats, SNPs, miRNA,... –Comparative genomics

19. Customizing tracks Tracks can be displayed in different levels of detail dense

20. FULL

22. Upload your own track You can upload your own track to the genome browser –As a file –As a URL pointing to a file –Data must be formatted in BED, GFF, GTF, WIG or PSL formats. Example: –You want to display miRNA target predictions in the genome browser

23. Export as high quality graphic It can be important, for example for a publication, to obtain high quality versions of the graphs displayed in the genome browser

24. Customizing the display Many details about the display can be customized

26. UCSC genome browser as data repository The genome browser is the front-end of a data repository The backend is a database that contains all the details about the displayed information The information in the databases can be retrieved seperately from the download section

29. ENSEMBL About the Ensembl Project Ensembl is a joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust.EMBLEuropean Bioinformatics InstituteWellcome TrustSanger InstituteWellcome Trust Goals of Ensembl The Ensembl project aims to provide: Accurate, automatic analysis of genome data. Analysis and annotation maintained on the current data. Presentation of the analysis to all via the web. Distribution of the analysis to other bioinformatics laboratories.

30. stat3

36. Summary The UCSC browser and the ENSEMBL browser have very similar functions It needs some time to get accustomed to any of them Remommendation: –Choose one of them –Get used to it –Stick to it

37. Summary cont’d They are highly flexible They allow to easily get an impression of a genomic region They are extremely powerful tools for –beginners as well as for experts –For biologists as well as Bioinformaticians

39. RIKEN Genomic Elements Viewer RIKEN provides the genomic elements viewer It was specifically developed to display the RIKEN CAGE data CAGE data provides infoemation about the start of a transcript And is very valuable for e.g. –Promoter analysis –Alternative regulation (isoforms)