The document outlines basic bioinformatics concepts, focusing on genome browsers and gene list interpretation facilitated by tools like Ensembl, UCSC, and NCBI. It emphasizes the integration of biological information through various databases, such as BioMart for retrieving and analyzing data, and provides insights into genome annotations and displays. Additionally, it introduces tools for analyzing gene lists, including DAVID, g:profiler, and Galaxy for data management.

1. Basic bioinformatics concepts, databases and tools Module 5 Genome browsers and interpretation of gene lists Dr. Joachim Jacob http://www.bits.vib.be Updated 21 July 2011 http://dl.dropbox.com/u/18352887/BITS_training_material/Link%20to%20mod5-intro_H1_2011_genomebrowsers.pdf

2. Integrating biological information Genome databases and browsers Integration on a species basis all biological information: Ensembl Genome Browser http://www.ensembl.org/ Table Browsers Retrieving biological (not only sequence) data applying various criteria: Biomart http://www.biomart.org/ Interpreting gene lists 'What is the biology behind my gene list': DAVID http://david.abcc.ncifcrf.gov/

3. Reference genome sequences provide a standard genome sequence per species Genomes From various sequence sources, a genome is assembled By NCBI: currently assembly 37 in human (or 'build') (2010) By Celera: commercial Each build differs! 1. Data freeze: all data for assembling (ignoring new data from that point) 2. Assembly process and annotation 3. Release of the Build: Reference Sequence Genom e http://www.ncbi.nlm.nih.gov/Genomes/

5. Finding your way in genomes Annotation and terms See also NCBI handbook Locus = place on the genome, ~ a gene (different alleles) Location: Rough location by staining of chromosomes e.g. 18q12.1 -> chromosome 18, long arm (=q, small arm is p) Exact bases on genomes (assembly must be mentioned!)

6. Genome Browsers: main players Three main players MapViewer (NCBI) UCSC Genome Browser Ensembl Genome browser BITS UCSC Genome Browser training BITS Ensembl Genome Browser training

7. Ensembl Genome browser We will use this browser in this session Information is combination of automatic annotation and manually curated s ources (ENS >< Havana (Vega) genes) All entries can be accessed through the browser, each with its own clear identifiers

8. 28 November 2009 [email_address] /10 http://www.ensembl.org Information about the genomes

9. http://www.ensemblgenomes.org

10. [email_address] /10 ! … or click on the figure feature!

11. 28 November 2009 [email_address] /10

12. 28 November 2009 [email_address] /10 [email_address]

13. TAB SUMMARY DETAILED INFORMATION INFOR-MATION SELEC-TOR DATA MANAGER tab DAS

14. Ensembl Genome browser Usefulness: One place for all information on a particular gene / structure / location / variation But also: Comparison to other species The Ensembl Team has a lot of training movies and examples available. Check them out! http://www.ensembl.org/info/index.html http://www.ensembl.org/Help/Movie?id=188

15. Ensembl Genome browser Usefulness: One place for all information on a particular gene / structure / location / variation But also: Comparison to other species The Ensembl Team has a lot of training movies and examples available. Check them out! http://www.ensembl.org/info/index.html http://www.ensembl.org/Help/Movie?id=188

16. Tracks are a way to display information on a genome sequence The annotation on a genome-wide scale is displayed in tracks. Relevant database content can be formatted in tracks and displayed on a reference genome Genome reference tracks Screenshot of Ensembl genome browser

17. Tracks are a way to display information on a genome sequence The annotation on a genome-wide scale is displayed in tracks, most used formats: - each base receives a value: dense continuous data: WIG format (e.g. %GC) - annotation has a start and a stop coordinate: bed format (e.g. gene annotations) Example Variations in genomes are reported in vcf format http://www.ensembl.org/info/website/upload/bed.html http://www.bits.vib.be/wiki/index.php/.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ

18. Biomart, your one stop portal to fetch information Biomart http://www.biomart.org/ These questions are easy: Hey, can you tell me how many genes in mouse exist which regulate transcription and are located on Chromosome 19 ?

19. Biomart, your one stop portal to fetch information Biomart http://www.biomart.org/ These questions are easy: Hey, can you tell me how many genes in mouse exist which regulate transcription and are located on Chromosome 19 ? Ensembl Genes Genome sequence (Ensembl) Gene Ontology GO:0009299

20. Biomart, your one stop portal to fetch information Biomart http://www.biomart.org/ Translated questions reflect in database choice and Filters Resulting genes are counted and the output set via Attributes

21. Biomart is available for an increasing number of databases Biomart http://www.biomart.org/

22. Gene lists resulting from different analyses can reveal their biology DAVID - http://david.abcc.ncifcrf.gov/

23. Gene lists resulting from different analyses can reveal their biology DAVID - http://david.abcc.ncifcrf.gov/ DEMO Alternatives g:Profiler http://biit.cs.ut.ee/gprofiler/ Babelomics http://www.babelomics.org/

24. Galaxy allows you to store your data and to (re)analyse it conveniently Galaxy - http://usegalaxy.org

25. Galaxy allows you to store your data and to (re)analyse it conveniently Galaxy - http://usegalaxy.org DEMO TOOLS RESULTS DATA SETS