Genome Viewing. Module 2. Using Genome Browsers to View Annotation of the Human Genome

Transcription

1 Module 2 Genome Viewing Using Genome Browsers to View Annotation of the Human Genome Bert Overduin, Ph.D. PANDA Coordination & Outreach EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK

2 Why Genome Browsers? Browse genes in their genomic context Display features in and around a particular gene Explore larger chromosomal regions Search and retrieve information on a genomewide scale Compare genomes

3 Genome Browsers Ensembl Genome Browser NCBI Map Viewer UCSC Genome Browser

4

5

6

7 What Distinguishes Ensembl? Automatic annotation for those species for which no manually annotated gene sets exist Data mining tool BioMart Direct database access and programmatic access via the Perl API Not only the data, but also the software code is open source

8 Ensembl - Organisation Joint project between the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) Started in 1999 for the Human Genome Project Funded primarily by the Wellcome Trust, with additional funding by EMBL, NIH-NHGRI, NIH- NIAID, BBSRC, MRC and EU Team of ca. 50 people, led by Ewan Birney (EBI) and Tim Hubbard (WTSI)

9 Ensembl - Species 48 chordates, ranging from human to two Ciona species 3 key eukaryote model organisms: Drosophila melanogaster Caenorhabditis elegans Saccharomyces cerevisiae

10 Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, 12 Drosophila species, 5 Caenorhabditis species, Ixodes scapularis Plasmodium falciparum, Plasmodium knowlesi, Plasmodium vivax Bacillus, Escherichia/Shigella, Mycobacterium, Neisseria, Pyrococcus, Staphylococcus, Streptococcus Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Oryza sativa indica group, Populus trichocarpa, Sorghum bicolor, Vitis vinifera 7 Aspergillus species, Neosartorya fischeri, Saccharomyces cerevisiae, Schizosaccharomyces pombe

11 Ensembl - Data Genomic sequence Gene / transcript / protein models External references Mapped cdnas, proteins, microarray probes, BAC clones, cytogenetic bands, repeats, markers etc. etc. Comparative data: orthologs and paralogs, protein families, whole genome alignments, syntenic regions Variation data: SNPs Regulatory data: best guess set of regulatory elements Externally stored data (Distributed Annotation System)

12 Ensembl Gene Models Automatically annotated genes for the whole genome of all species ( Ensembl genes ) Manually annotated genes for part of the human and mouse genome ( Vega/Havana genes)

13 Biological Evidence All Ensembl gene models are based on evidence from: UniProtKB/Swiss-Prot Proteins, manually curated NCBI RefSeq Proteins and mrnas, partially manually curated UniProtKB/TrEMBL Translations of EMBL-Bank CDSs, automatically annotated EMBL-Bank / GenBank / DDBJ Primary nucleotide sequence repositories

14 Ensembl Genebuild Genome assembly + Experimental evidence + Computer programs

15 Access to Data Release web site Pre-release web site Archive web site BioMart FTP site ftp://ftp.ensembl.org Amazon Web Services MySQL Perl API

16 Ensembl Stable Identifiers Human: ENSG########### Ensembl Gene ID ENST########### Ensembl Transcript ID ENSP########### Ensembl Protein ID ENSE########### Ensembl Exon ID ENSR########### Ensembl Regulatory Feature ID ENSSNP########### Ensembl SNP ID ENSFM########### Ensembl Protein Family ID Other species have a suffix: ENSMUSG########### A mouse (Mus musculus) gene

17 Summary Genome browsers render the plain sequence more accessible Ensembl provides automatic genome annotation, yet is strongly based on experimental evidence from protein and cdna sequences in public databases Ensembl heavily links to data sets from other species, as well as to external resources

18 Data Mining Ensembl with BioMart

19 BioMart Joint project between the European Bioinformatics Institute (EBI) and the Ontario Institute for Cancer Research (OICR) Originally developed for Ensembl (EnsMart) Website :

20 Publicly Available Marts Ensembl Ensembl Bacteria Ensembl Metazoa Ensembl Protists Dictybase Wormbase Gramene Europhenome UniProt InterPro HGNC Rat Genome Database DroSpeGe ArrayExpress DW Eurexpress HapMap GermOnLine PRIDE PepSeeker VectorBase HTGT Pancreatic Expression Database Reactome EU Rat Mart Paramecium DB International Potato Center (CIP) Central portal:

21 BioMart - Principle Step 1 Dataset Choose your dataset and species Step 2 Filters Limit your dataset Step 3 Attributes Specify what information you want to output Step 4 Results Preview and output your results

22 Summary BioMart is a highly flexible tool for data mining Queries are defined in just 4 steps: Dataset, Filters, Attributes and Results Genomic regions, Gene identifiers, Gene Ontology terms and many other sources of information can serve as filters BioMart heavily links to data sets within Ensembl and provides links to external resources

23 Help Helpdesk Mailing lists: Blog: YouTube channel:

24

25