phylogenetic prediction of gene function
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Phylogenetic prediction of gene function
Daniel BarkerCentre for Evolution, Genes and Genomics,
School of Biology,
University of St Andrews
http://biology.st-andrews.ac.uk/cegg
1 0 1 0 1 0 1 01 0 1 0 1 0 1 0
1 1 1 1 0 0 0 01 1 1 1 0 0 0 0
1 0 1 0 1 0 1 01 0 1 0 1 0 1 0
1 1 1 1 0 0 0 01 1 1 1 0 0 0 0
Gene A 1 0 1 0 1 0 1 0Gene B 1 0 1 0 1 0 1 0
Gene C 1 1 1 1 0 0 0 0Gene D 1 1 1 1 0 0 0 0
sp. i
sp. i
i
sp. i
ii
sp. i
v
sp. v
sp. v
i
sp. v
ii
sp. v
iii
Correlations in gene gain/loss
0.1
S. cerevisiaeS. paradoxus
S. mikatae
S. bayanus
S. castellii
Saccharomyces kluyveri
Candida albicans
Schizosaccharomyces pombe
Fusarium graminearum
Neurospora crassa
Magnaporthe griseaAspergillus nidulans
Cryptococcus neoformans
Drosophila melanogaster
Caenorhabditis elegans
1 1 0 0
1 1 0 0
1 1 0 0
1 1 0 0
1 1 0 0
1 1 1 11 1 1 1
0 1 1 1
0 0 0 1
0 0 0 1
0 0 1 1
0 0 0 1
0 0 0 1
0 0 0 1
0 0 0 1
CIN4
ORC3L9A
L42B
0.1 changesper nucleotide
The ‘traditional’ across-species method of phylogenetic profiles (Pellegrini et al. 1999, PNAS 96: 4285–7288) returns a false positive functional link for the pair of proteins {CIN4, ORC3} and a false negative for the pair {L9A, L42B}. The tree-based, maximum likelihood phylogenetic method returns the ‘correct’ result for both pairs (Barker & Pagel 2005, PLoS Comp Biol 1:24–31).
Example
1.0 0.5
0.2
0.1
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p-value cut-off
30
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20
% s
pec
ific
ity
Validation
Test data based on known yeast protein complexesIn the Comprehensive Yeast Genome Database(http://mips.gsf.de/genre/proj/yeast)
University of Reading:Mark PagelAndrew Meade
Wellcome Trust Sanger Institute:Valerie Wood
(UCL):Antonio Cavallo
Funding:BBSRC
EPSRC on behalf of Research Councils UK
Acknowledgements
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