Document Detail


In silico phenotypic screening method of mutants based on statistical modeling of genetically mixed samples.
MedLine Citation:
PMID:  16374907     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
In comprehensive functional genomics projects, systematic analysis of phenotypes is vital. However, conventional phenotypic screening is done mainly by imprecise visual observation of qualitative traits, and, therefore, in silico screening techniques for quantitative traits are required. In this report, we propose in silico phenotypic screening method that utilizes a Gaussian mixture model for the trait distribution in the offspring of a mutagenized line and the likelihood ratio test between the estimated Gaussian mixture model and the wild-type single Gaussian model. In order to evaluate the proposed method, we performed a screening experiment using real trait data of Arabidopsis. In this experiment, the proposed screening method properly distinguished the mutant line from the wild-type line. Furthermore, we conducted power analysis of the proposed method and two conventional methods under various simulated conditions of sample size and distribution of trait frequency. The result of the power analysis confirmed the effectiveness of the proposed method compared to the conventional methods.
Authors:
Eli Kaminuma; Naohiko Heida; Takeshi Yoshizumi; Miki Nakazawa; Minami Matsui; Tetsuro Toyoda
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Journal of bioinformatics and computational biology     Volume:  3     ISSN:  0219-7200     ISO Abbreviation:  J Bioinform Comput Biol     Publication Date:  2005 Dec 
Date Detail:
Created Date:  2005-12-23     Completed Date:  2006-03-21     Revised Date:  2009-11-19    
Medline Journal Info:
Nlm Unique ID:  101187344     Medline TA:  J Bioinform Comput Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  1281-93     Citation Subset:  IM    
Affiliation:
Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan. eli@gsc.riken.jp
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Arabidopsis / genetics
Chromosome Mapping / methods*
Computer Simulation
DNA Mutational Analysis / methods*
Genetic Testing / methods
Genetic Variation / genetics*
Models, Genetic*
Models, Statistical
Phenotype*
Quantitative Trait Loci / genetics*
Sequence Alignment / methods
Sequence Analysis, DNA / methods
Comments/Corrections
Erratum In:
J Bioinform Comput Biol. 2006 Feb;4(1):169

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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