http://creativecommons.org/licenses/by-sa/2.0/

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http//creativecommons.org/licenses/by-sa/2.0/
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EnsemblDatabase and Web Browser
Erin Pleasance Canadas Michael Smith Genome
Sciences Centre, Vancouver
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www.ensembl.org
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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 (ChromoView, KaryoView, CytoView,
MapView)
SNPs and Haplotypes (SNPView, GeneSNPView, HaploVi
ew, LDView)
Sequence Similarity (BLAST, SSAHA)
Diseases (DiseaseView)
Genome Sequence (ContigView)
Genes (GeneView, TransView, ExonView, ProtView)
Markers (MarkerView)
Functions (GOView)
Text (TextView)
Other Annotations
Families (DomainView, FamilyView
Anything (EnsMart)
Comparative Genomics (ContigView,
MultiContigView, SyntenyView, GeneView)
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Species in Ensembl

• Focus on vertebrates
• No fungi/plants
• Arabidopsis genome browser based on Ensembl at
  http//atensembl.arabidopsis.info/

Vertebrates
Invertebrates
Mammals Human Chimp Mouse Rat Dog Cow Opossum
Insects Fruitfly Mosquito Honeybee
Fish Zebrafish Fugu Pufferfish Tetraodon
Pufferfish
Other Chicken Frog
Other Nematode
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Ensembl Gene Annotation

• Basis for initial analysis and publication of
  most vertebrate genomes
• Genome assembly from NCBI
• Gene build system
• Targetted 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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Targetted gene build

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

UTRs predicted
Known gene (p53)
ContigView of best in genome gene with associated
evidence
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

ContigView of homology gene with associated
evidence
Unigene clusters aligned
Proteins aligned
Novel gene
GenScan predictions
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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

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Manually curated genes VEGA

• Some chromosomes contain manually curated genes
  from VEGA database
• Otter database/server allows integration of
  automatic and manual annotations (eg. from
  Apollo)

VEGA gene
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Ensembl EST genes

• ESTs not accurate enough to produce Ensembl
  genes, but important especially 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

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Example 1 Exploring Caspase-3
http//www.ensembl.org
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Species-specific homepage
Site map
Statistics of current release
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Finding the tool/view Site Map
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Text Search
Click Back to
Species-specific homepage
Gene
caspase-3
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GeneView
ContigView
ExportView
SNPView
ProteinView
ExonView
TransView of transcript
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GeneView
Orthologs predicted by sequence similarity and
synteny
GeneDAS Get data from external sources
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GeneView
On the same page, information provided for each
transcript individually
Links to external databases
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GeneView
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GeneSNPView
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Other SNP/Haplotype tools

• SNPView
• 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
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ContigView Detailed View
Genscan predictions
Targetted gene predictions (2 alternative
transcripts)
Gene annotations
EST genes
Other tracks Aligned sequences etc.
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ContigView
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MultiContigView
DNA sequence homology
Rat ortholog
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Other Comparative Genomics Tools

• Saw gene orthology, DNA homology
• Other view is SyntenyView
• Also access comparative genomics through EnsMart

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Data Mining with EnsMart

• 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 EnsMart

• 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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Example 2 EnsMart

• EnsMart is based on BioMart
• http//www.ensembl.org/Multi/martview
• OR
• http//www.ebi.ac.uk/BioMart/martview

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EnsMart Choosing your dataset
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EnsMart Filtering
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D21S1991
D21S171
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EnsMart Output
Note you can output different types of
information eg. sequences
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EnsMart 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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Finding anything else 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
• Some built-in DAS sources
• http//www.ensembl.org/Docs/ ldas.html

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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

Sockeye
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For more information

• Publications (listed at http//www.ensembl.org/Doc
  s/ wiki/html/EnsemblDocs/EnsemblPublications.html)
  
• Ensembl Special Genome Research May 2004
• Ensembl updates NAR Jan. 2002-2005
• EnsMart Kasprzyk et al, Genome Res Jan. 2004
• Documentation on how to download software and
  database
• http//www.ensembl.org/Docs/

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Exercises

• 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?
• 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 EnsMart, the GO term for apoptosis is
  GO0006915, evidence code TAS
• The file PCR_product.txt 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?