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11 Feb 2011, Science, Cover

11 Feb 2011, Science, Cover. 12 Feb 2011 Science. Deluge of genomic data. but it ’ s computable. Sea of phenomic data. not yet computable. Translation?. Pimelodus maculatus. photo J. Lundberg, ANSP 2002. Genes are conserved across divergent phenotypes.

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11 Feb 2011, Science, Cover

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  1. 11 Feb 2011, Science, Cover

  2. 12 Feb 2011 Science Deluge of genomic data but it’s computable...

  3. Sea of phenomic data... not yet computable

  4. Translation? Pimelodus maculatus photo J. Lundberg, ANSP 2002

  5. Genes are conserved across divergent phenotypes Used with permission from Micromundi: http://remf.dartmouth.edu/images/ MicromondiImages/16chrysomelidae220.tif Courtesy of Kevin Helenurm

  6. Translational medicine Fig. 1, Washington et al., 2010 Translation from model organisms to humans

  7. Phenotype ontologies enable discovery Evolutionary phenotypes from species Gene phenotypes from mutants

  8. Phenotype extracted from literature

  9. Phenotype annotation of gene Zebrafish Gene Ontology wild type Zebrafish Anatomy Ontology (2196 terms; 310 skeletal) Quality Ontology (1,075 terms) Quality Ontology (1,323 terms) mutant http://zfin.org/cgi-bin/webdriver?MIval=aa-fxfigureview.apg&OID=ZDB-FIG-070117-784

  10. Phenotype annotation of taxon Teleost Taxonomy Ontology (38,590 terms; 59,664 synonyms) species 1 species 1 Teleost Anatomy Ontology (3,037 terms; 618 skeletal) Quality Ontology (1,323 terms) species 2

  11. sequence-specific DNA binding transcription factor activity tfap2a olfactory region ethmoid cartilage chondrocranium cartilage Brachyplatystoma round Pimelodidae shape variant_of has_function part_of is_a inheres_in is_a is_a is_a is_a is_a split inheres_in is_a Reasoning across logical relationships Brachyplatystoma capapretum round that inheres_insome ethmoid cartilage exhibits some split that inheres_insome ethmoid cartilage tfap2ats213/ts213 influences some

  12. image:http://www.ustacrosport.com/buried-treasure 500,000 testable hypotheses... kb.phenoscape.org

  13. 21,829 gene phenotypes for 3,893 genes 501,862 taxon phenotypes Phenoscape Knowledgebase Interative user testing of interface kb.phenoscape.org

  14. Gill rakers, absent Are gill rakers absent in eels because of changes in regulation of the eda pathway? Harris et al., 2008 taxa: genes: eda, edar, (195) (2) Anguilliforms,some catfish, e.g., Sisor rabdophorus, Chaca chaca

  15. Lateral line, incomplete or absent Is the reduced lateral line in Minytrema the result of pcsk5a mutation? Smith, 1992 Chitramuthu et al., 2010 erbb3b, eya1, pcsk5a, rog, sox10, unm_m583 taxa: genes: (6) (102) Minytrema,Mullidae,Wolf eels

  16. Caudal fin, absent Did Mola lose its caudal fin because of changes in regulation of yap1? Jiang et al., 2009 Britz & Johnson, 2005 taxa: genes: smc3, tll1, yap1 (25) (3) Mola,Gymnotiformes

  17. Ceratobranchial 5 teeth, absent Is loss of teeth in Gyrinocheilus related to changes in regulation of eda? eda, edar, http://www.brettb.com/images/AlgaeLoach2.jpg Harris et al., 2008 taxa: genes: (30) (2) Tetraodontidae, Chanos, Gyrinocheilus,Liparidaesome Characiformes, etc.

  18. Dorsal fin, absent develops_from Median finfold Is the loss of a dorsal fin in South American knifefishes connected to tfap2a? hoxa13a, tfap2a Li et al., 2007 Fink & Fink, 1981 genes: taxa: Gymnotiformessome silurids (2) (58)

  19. Global view of skeletal data viewed, summarized, synthesized, at a scale not possible otherwise. Image from Sabaj-Perez Skeletal variation across taxa and regions

  20. Summary • Genes mapped to taxa via phenotype • Candidate genes • Candidate taxa • Powerful approach for data synthesis and discovery • Makes data accessible for broad group of researchers and creates opportunities for new and synthetic research • Future: ‘phenoblast’ search; vertebrates; homology

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