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Genome and Proteome Annotation Using Automatically Recognized Concepts and Functional Networks

Genome and Proteome Annotation Using Automatically Recognized Concepts and Functional Networks

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Published by AMIA
2013 Summit on Translational Bioinformatics
2013 Summit on Translational Bioinformatics

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Categories:Types, Research
Published by: AMIA on Apr 09, 2013
Copyright:Attribution Non-commercial

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03/05/2014

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Genomeandproteomeannotationusingautomaticallyrecognizedconceptsandfunctionalnetworks
AdrianBivol,
TobiasWittkop
,DarcyDavis,andSeanMooneyMooneylaboratory,BuckInstituteforResearchonAging,Novato,CANationalCenterforBiomedicalOntology,StanfordUniversity,Stanford,CA
 
Genefunction/diseaseprediction
Typically uses Gene Ontology (GO) or disease annotation (e.g. OMIM)Many tools utilize similar set of features/networks, e.g. PPI networks,co-expression networks, sequence similarity,...Input: Set of genes with known function/diseaseOutput: ranked list of remaining genes (closest at the top)
Can these tools be used for other annotations then GO or disease?
 
Systematicevaluationofautomatedannotations
1.
Annotate all (human) genes
 
to terms
from ontologiesoutside GO and OMIM, e.g. Phenotype Ontology,CHEBI, or Pathway Ontology.2.
For each term (gene set) evaluate “predictability”,
i.e. how well can we predict the genes that areannotated to it using existing gene function predictionmethods.

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