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Ensembl
Database and Web Browser
www.ensembl.org
Stephen Baird
Apoptosis Research Centre
Children’s Hospital of Eastern Ontario
[email protected]
Lecture/Lab 7.3
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Lecture 7.1
Focus on vertebrates
No fungi/plants
Brassica/Arabidopsis
genome browser is at
http://ensembl.warwick.ac.uk/
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What is Ensembl?
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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
Lecture/Lab 7.3
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Ensembl components
Search tools:
Data:
Chromosomes
(FeatureView, KaryoView,
Ctyoview, MapView)
Diseases
SNPs and Haplotypes
(SNPView, GeneSNPView,
HaploView, LDView)
(DiseaseView)
Functions
(GOView)
Sequence
Similarity
(BLAST, SSAHA)
Genes
(GeneView, TransView,
ExonView, GeneSeqView)
Protein
(ProtView, DomainView,
FamilyView
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Genome
Sequence
Markers
(MarkerView)
(ContigView)
Comparative
Genomics
(ContigView, MultiContigView,
SyntenyView, GeneView)
Text
(TextView)
Other
Annotations
Anything
(BioMart/Martview)
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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
UTRs predicted
ContigView of best in genome
gene with associated evidence
Known gene (p53)
Proteins aligned
Unigene clusters aligned
Lecture/Lab 7.3
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
Unigene
ContigView of homology gene with
clusters
associatedaligned
evidence
Proteins aligned
GenScan predictions
Lecture/Lab 7.3
Novel gene
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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
Lecture/Lab 7.3
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:
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Gene annotation
SNPs
Orthologs and genome alignments
Alternative transcripts and EST genes
Protein Structure
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Species-specific
homepage Gene
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Text Search
caspase-3
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GeneView
GeneSplice
View
GeneRegulation
View
ContigView
GeneSNPView
ExportView
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TransView
of transcript
ExonView
ProteinView
Orthologs predicted
by sequence
similarity and16
synteny
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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Click Back to
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GeneView
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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
Gene
annotations
Targetted gene
predictions
(2 alternative
transcripts)
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
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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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D21S1991
D21S171
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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
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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 ‘Manage
sources’ in
DAS dropdown
menu
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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/
Lecture/Lab 7.3
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 GO:0006915, 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?
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