PhyloPat2 - Department of Computing Science
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Transcript PhyloPat2 - Department of Computing Science
PHYLOPAT: AN UPDATED VERSION
OF THE PHYLOGENETIC
PATTERN DATABASE CONTAINS GENE
NEIGHBORHOOD
Tim Hulsen et.al.,
Nucleic Acids Research, 2009, Vol. 37, Database issue
Presenter: Reihaneh Rabbany
Presented in Bioinformatics Course (CMPUT 606),
Instructed by Prof. Guohui Lin,
Computing Science Department,
University of Alberta,
Winter 2009
INTRODUCTION
Phylogenetic patterns
Show the presence or absence of certain genes
in a set of whole genome sequences
Can be used to determine sets of genes that
occur only in certain evolutionary branches
More Common as increasing amounts of
orthology data have become available
Phylogenetic Patterns Search tools are available
for querying proteins, but not for querying genes
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PHYLOPAT
PhyloPat is a database which offers the
possibility of querying the Ensembl database
using any phylogenetic pattern
Functionalities :
Gene neighborhood view
Anticorrelating patterns
Support of Entrez ‘ Gene IDs
Direct sequence retrieval of members of a
phylogenetic lineage
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ENSEMBL
Human genome
3 billion base-pairs
35,000 genes
The genome alone is of little use
Locations and relationships of individual genes
Manual annotation
Ensembl
Ensembl (freely accessible)
Sequence data is fed into a software "pipeline“
Creates a set of predicted gene locations
Saves them in a MySQL database
Originally focus on Human
Now includes mouse, fruitfly, zebrafish, plants, fungi, …
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PHYLOPAT - DATABASE CONTENT
A set of phylogenetic lineages
Complete set of orthologies Collected
All 39 species’ genes in Ensembl
741 species pairs
815 452 genes
19 010 478 orthologous relationships
11 446 546 one-to-one
4 588 300 one-to-many
2 975 632 many-to-many
Ensembl ortholog detection pipeline
Similarity values by
Best reciprocal hits and best score ratio (WU BLASTP)
Graph of gene relations and Clustering
Multiple alignment (MUSCLE )
Phylogenetic tree (TreeBeST )
Orthologous relationships
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PHYLOPAT - DATABASE CONSTRUCTION
Generating phylogenetic lineages
Determining evolutionary order
Using the NCBI Taxonomy
Phylogenetic tree Phylogenetic lineages
For each gene in the first species
Look for orthologs in the other species
Add all orthologs to the phylogenetic lineage
Check for orthologs themselves, until no additional
orthologies were found for any of the genes
Repeat for all genes in all 39 species that were
not yet connected to any phylogenetic lineage
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WEB APPLICATION
A web interface
Query the PhyloPat MySQL database
Phylogenetic lineages
Phylogenetic patterns
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OMNIPRESENT - OLIGOPRESENT POLYPRESENT GENES
Omnipresent
Genes present in all 39 species
688 omnipresent genes
Which most likely have important functions, since they are
present in all species.
Oligopresent
Genes that exist in only one or two species
phylogenetic pattern
‘11111111111111111111111111111111111111’ (or MySQL
regular expression ‘^1+$’)
Which species are evolutionary most related
Polypresent
Genes that are missing in only one or two species
Measure for evolutionary relatedness
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ANTICORRELATING PATTERNS
Patterns that are exactly opposite
Phylogenetic lineages with anticorrelating
patterns can be functionally completely different,
but could also be highly similar in function
‘000000000000000010111001111001111110010’
‘111111111111111101000110000110000001101’
These genes can be analogous i.e. performing a
similar function without being evolutionary
related.
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GENE NEIGHBORHOOD
Inferring ‘true’ orthology
Orthologous conservation of gene neighborhood
Human gene ENSG00000134398
Has two predicted orthologs in chimpanzee:
gene ENSPTRG00000007893
gene ENSPTRG00000009535
Only correspond to the gene neighborhoods of gene
ENSPTRG00000007893, for nine of the nearest neighbors
Inferring functional annotation
Build hypotheses about the processes or
pathways that genes might be involved in
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FASTA-FORMAT SEQUENCE FILES
Both the pattern search output and the gene
neighborhood view contain links to FASTA files
of the peptide sequences
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DISCUSSION AND CONCLUSION
PhyloPat is useful in
Orthology detection
Evolutionary studies
Gene annotation
Complex Queries
It is possible to determine
A species set that should be included (1),
A species set that should be excluded (0)
A species set which presence is indifferent (*)
Using of regular expression queries
Easy-to-use web interface
Relies only on one database (Ensembl)
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DISCUSSION AND CONCLUSION (CONT.)
Gene neighborhood view
Locating evolutionary-related genomic clusters of
genes
Detecting the ‘true orthologs’ within large sets of
predicted orthologs
Functional annotating less well known genes
PhyloPat will be updated with each major
Ensembl release to ensure up-to-date and reliable
phylogenetic lineages (species added)
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LINEAGE INFORMATION OF PP000255
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QUESTIONS
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