Download - 11 Feb 2011, Science, Cover
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11 Feb 2011, Science, Cover
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12 Feb 2011 Science
Deluge of genomic data but it’s
computable...
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Sea of phenomic data... not yet
computable
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Translation?
photo J. Lundberg, ANSP 2002Pimelodus maculatus
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Genes are conserved across divergent phenotypes
Courtesy of Kevin HelenurmUsed with permission from Micromundi: http://remf.dartmouth.edu/images/MicromondiImages/16chrysomelidae220.tif
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Fig. 1, Washington et al., 2010
Translational medicine
Translation from model organisms to humans
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Phenotype ontologies enable
discoveryEvolutionary phenotypes
from species
Gene phenotypes
from mutants
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Phenotype extracted from literature
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Phenotype annotation of gene
wild type
Zebrafish
GeneEntity
Quality
fam32al
Head Small size
Eye Small size
Ventral mandible Thick
Heart Edematous
Quality Ontology
(1,075 terms)
Gene Ontology
Zebrafish Anatomy Ontology
(2196 terms; 310 skeletal)
Quality Ontology
(1,323 terms) mutant
http://zfin.org/cgi-bin/webdriver?MIval=aa-fxfigureview.apg&OID=ZDB-FIG-070117-784
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Phenotype annotation of taxon
species 1
TaxonEntity
Quality
species 1Head cylindrical
Adipose fin absent
species 2Head flat
Adipose fin present
Quality Ontology
(1,323 terms)
Teleost Taxonomy Ontology
(38,590 terms;59,664 synonyms)
Teleost Anatomy Ontology
(3,037 terms; 618 skeletal)
species 1
species 2
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Brachyplatystoma capapretum
round thatinheres_in some
ethmoid cartilage
exhibits some
tfap2ats213/ts213split that
inheres_in someethmoid cartilage
influences some
round
split
ethmoid cartilageBrachyplatystom
a
tfap2a
is_a
variant_of inheres_
in
inheres_in
is_a
is_a
shape
chondrocranium cartilage
olfactory region
Pimelodidae
sequence-specific DNA binding
transcription factor activity
is_a
has_function is_a part_of
is_ais_a
Reasoning across logical relationships
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500,000 testable hypotheses...
image:http://www.ustacrosport.com/buried-treasure
kb.phenoscape.org
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Phenoscape Knowledgebase
501,862 taxon phenotypes
21,829 gene phenotypes for
3,893 genes
kb.phenoscape.org
Interativeuser
testing ofinterface
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Anguilliforms,some catfish, e.g., Sisor rabdophorus, Chaca chaca
Harris et al., 2008
Gill rakers, absent
eda, edar,
taxa:
genes:
Are gill rakers absent in eels because of
changes in regulation of the eda pathway?
(2)(195)
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Minytrema,Mullidae,Wolf eels
Chitramuthu et al., 2010
Smith, 1992
Lateral line, incomplete or absent
erbb3b, eya1,
pcsk5a, rog,
sox10, unm_m58
3
taxa: genes:
Is the reduced lateral line in Minytrema the
result of pcsk5a mutation?
(6)(102)
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Mola,Gymnotiformes
Jiang et al., 2009
Britz & Johnson, 2005
Caudal fin, absent
smc3,
tll1,yap1
taxa:
genes:
Did Mola lose its caudal fin because of changes in regulation
of yap1?
(25) (3)
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Tetraodontidae, Chanos, Gyrinocheilus,Liparidaesome Characiformes, etc.
Ceratobranchial 5 teeth, absent
eda, edar,
taxa: gen
es:Harris et al., 2008
http://www.brettb.com/images/AlgaeLoach2.jpg
Is loss of teeth in Gyrinocheilus related
to changes in regulation of eda?
(2)(30)
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Gymnotiformessome silurids
Li et al., 2007Fink & Fink, 1981
Dorsal fin, absent
hoxa13a,
tfap2a
taxa:
genes:
Median finfold
Is the loss of a dorsal fin in South
American knifefishes connected to tfap2a?
(2)(58)
develops_from
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Global view of skeletal data
Image from Sabaj-Perez
Skeletal variation across taxa and regions
viewed, summarized, synthesized, at a scale not possible otherwise.
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Summary1.Genes mapped to taxa via phenotype
• Candidate genes • Candidate taxa
2.Powerful approach for data synthesis and discovery
3.Makes data accessible for broad group of researchers and creates opportunities for new and synthetic research
4.Future: ‘phenoblast’ search; vertebrates; homology
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