Ensembl Database and Web Browser www'ensembl'org

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EnsemblDatabase and Web Browserwww.ensembl.org
Stephen Baird Apoptosis Research
Centre Childrens Hospital of Eastern
Ontario sbaird_at_arc.cheo.ca
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• Focus on vertebrates
• No fungi/plants
• Brassica/Arabidopsis genome browser is at
  http//ensembl.warwick.ac.uk/

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What is Ensembl?

• Joint project of EBI and Sanger
• Automated annotation of eukaryotic genomes
• Open source software
• Relational database system
• Web interface

The main aim of this campaign is to encourage
scientists across the world - in academia,
pharmaceutical companies, and the biotechnology
and computer industries - to use this free
information.
- Dr. Mike Dexter, Director of the Wellcome Trust
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Ensembl components
Search tools
Data
Chromosomes (FeatureView, KaryoView, Ctyoview,
MapView)
SNPs and Haplotypes (SNPView, GeneSNPView, HaploVi
ew, LDView)
Sequence Similarity (BLAST, SSAHA)
Diseases (DiseaseView)
Genome Sequence (ContigView)
Genes (GeneView, TransView, ExonView, GeneSeqView)
Markers (MarkerView)
Functions (GOView)
Text (TextView)
Other Annotations
Protein (ProtView, DomainView, FamilyView
Anything (BioMart/Martview)
Comparative Genomics (ContigView,
MultiContigView, SyntenyView, GeneView)
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Ensembl Gene Annotation

• Basis for initial analysis and publication of
  most vertebrate genomes
• Genome assembly from NCBI
• Gene build system
• Targeted gene builds predict known genes
• Similarity gene builds predict novel genes

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Curwen et al, Genome Res 14 942-950, 2004
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Targeted gene build

• Align known proteins with pmatch and BLAST
• Incorporate aligned cDNA sequences to find splice
  sites, UTRs with genewise

ContigView of best in genome gene with associated
evidence
UTRs predicted
Known gene (p53)
Proteins aligned
Unigene clusters aligned
cDNAs aligned
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Similarity gene build

• Identify novel exons ab initio using Genscan
• Confirm exons by BLAST to known proteins, mRNAs,
  UniGene clusters

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Ensembl Gene Annotation

• Resulting Ensembl genes are highly accurate
  with low false positive rates
• Ensembl human gene identifiers are 95 stable
  between builds
• Ensembl and RefSeq differ with 8-12 of the
  genes
• The Consensus CDS (CCDS) project is a
  collaborative effort between Ensembl/EBI, UCSC
  and NCBI to identify a core set of human protein
  coding regions that are consistently annotated
  and of high quality (13,000 genes).

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Manually curated genes VEGA

• Some chromosomes contain manually curated genes
  from VEGA database
• Otter manual annotation system allows
  integration of automatic and manual annotations
  (eg. from Apollo) into Ensembl by The Human and
  Vertebrate Annotation (HAVANA) group annotators
  at the Sanger center

VEGA gene
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Ensembl EST genes

• ESTs not accurate enough to produce Ensembl
  genes, but important for identifying alternative
  transcripts
• ESTs aligned to genome and merged to create an
  independent set of EST genes

Known gene
EST genes
Unigene clusters aligned
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Pseudogenes

• Processed pseudogenes in annotation identified
  (lack of introns, frameshifts, presence of
  multi-exon version elsewhere in genome, etc.)

Pseudogene
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Noncoding RNA Genes

• Genes with no ORFs that are functional (tRNAs,
  rRNAs, miRNAs )
• 7220 annotations from Sean Eddy and Tom Jones

miRNAs
Coding gene
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Example 1 Exploring Caspase-3

• Aim to demonstrate basic browsing and views
• Caspase-3 is a gene involved in apoptosis (cell
  suicide)
• We will look at
• Gene annotation
• SNPs
• Orthologs and genome alignments
• Alternative transcripts and EST genes
• Protein Structure

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Text Search
Species-specific homepage
caspase-3
Gene
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GeneView
GeneSpliceView
GeneRegulationView
ContigView
GeneSNPView
ExonView
TransView of transcript
ProteinView
ExportView
Orthologs predicted by sequence similarity and
synteny
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GeneView
DAS - Distributed Annotation System - external
annotation of splicing, transcripts, array
expression, pubmed links, associated phenotypes,
Protonet, Reactome, UniProt.
Information for each Transcript - similarity
matches, links to RefSeq, OMIM, PDB, Array
probes, GO, InterPro, Protein FamilyView,
transcript structure, protein properties.
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GeneView
GeneSNPView
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GeneSNPView
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Other SNP/Haplotype tools

• SNPView info on a single SNP
• ProteinView (protein sequence with SNP markup)
• LDView View linkage disequilibrium (only limited
  regions)
• HaploView View haplotypes (only limited regions)

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GeneView
Click Back to
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ContigView
Chromosome and bands
Sequence contigs
To Detailed view
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ContigView Detailed View
See other tracks, options in menus
Genscan predictions
Targetted gene predictions (2 alternative
transcripts)
Gene annotations
EST genes
Other tracks Aligned sequences etc.
Base View Region
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ContigView- Features menu
Export image (ps, pdf, svg) or fasta file
Click on close menu
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MultiContigView
Conserved regions
Rat ortholog
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Other Comparative Genomics Tools

• Up to 6 genome alignments with MLAGAN in
  AlignSliceView
• Other view is SyntenyView
• Also access comparative genomics through EnsMart

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DAS-Distributed Annotation System
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Data Mining with BioMart

• Allows very fast, cross-data source querying
• Search for genes (features, sequences, etc.) or
  SNPs based on
• Position function domains similarity
  expression etc.
• Accessible from Ensembl website (MartView) as
  well as stand-alone
• Extremely powerful for data mining

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Example 2 BioMart

• A new disease locus has been mapped between
  markers D21S1991 and D21S171. It may be that the
  gene involved has already been identified as
  having a role in another disease. What candidates
  are in this region?

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BioMart Choosing your dataset
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BioMart Filtering
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BioMart Output
Note you can output different types of information
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BioMart Output
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Sequence Similarity Searching

• Use SSAHA for exact matches (fast)
• Use BLAST for more distant similarity (slow)

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Looking for Help?
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DAS Getting your Own Data in Ensembl

• DAS (Distributed Annotation System)
• Anyone can load data into Ensembl and allow
  others to view it in the same view (eg.
  ContigView) as other Ensembl annotations
• Click on Managesources in DAS dropdownmenu

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Other Ways to Access Ensembl

• MySQL database directly accessible
• APIs for Perl and Java

• Other software
• Apollo Java genome annotation viewer/editor
• Sockeye Java viewer
• You can get your own local version of Ensembl
  software and data freely available
• http//www.ensembl.org/Docs/

Sockeye
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Exercises

• Ex 1. Homologues of human genes are often present
  in Fugu rubripes in more condensed form (with
  shorter introns). Is this true for the gene PTEN,
  a tumor suppressor often mutated in advanced
  cancers?
• Try MultiContigView can you think of another way
  to get this information as well?
• Ex 2. The microRNA bantam regulates the
  Drosophila (fruitfly) gene hid by binding the 3
  UTR. Hid is involved in apoptosis, and it is
  possible that binding sites for bantam could be
  found in the 3 UTR of other apoptosis genes as
  well. Obtain the 3 UTR sequence of all
  Drosophila genes known to be involved in
  apoptosis.
• Using BioMart, the GO term for apoptosis is
  GO0006915, evidence code TAS
• Ex 3. The file PCR_product.txt on the webserver
  contains the sequence of a PCR product amplified
  from a mouse cDNA library. What gene does the
  product correspond to? Does it contain the
  complete coding sequence of that gene?
• Would it be better to use BLAST or SSAHA?