Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study

Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregular sampling. In this paper three popular spectral analysis schemes, namely, Lomb-Scargle, C...

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Detalles Bibliográficos
Autores principales: Zhao, Wentao, Agyepong, Kwadwo, Serpedin, Erchin, Dougherty, Edward R
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer 2008
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171399/
https://www.ncbi.nlm.nih.gov/pubmed/18584052
http://dx.doi.org/10.1155/2008/769293
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author Zhao, Wentao
Agyepong, Kwadwo
Serpedin, Erchin
Dougherty, Edward R
author_facet Zhao, Wentao
Agyepong, Kwadwo
Serpedin, Erchin
Dougherty, Edward R
author_sort Zhao, Wentao
collection PubMed
description Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregular sampling. In this paper three popular spectral analysis schemes, namely, Lomb-Scargle, Capon and missing-data amplitude and phase estimation (MAPES), are compared in terms of their ability and efficiency to recover periodically expressed genes. Based on in silico experiments for microarray measurements of Saccharomyces cerevisiae, Lomb-Scargle is found to be the most efficacious scheme. 149 genes are then identified to be periodically expressed in the Drosophila melanogaster data set.
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spelling pubmed-31713992011-09-13 Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study Zhao, Wentao Agyepong, Kwadwo Serpedin, Erchin Dougherty, Edward R EURASIP J Bioinform Syst Biol Research Article Time series microarray measurements of gene expressions have been exploited to discover genes involved in cell cycles. Due to experimental constraints, most microarray observations are obtained through irregular sampling. In this paper three popular spectral analysis schemes, namely, Lomb-Scargle, Capon and missing-data amplitude and phase estimation (MAPES), are compared in terms of their ability and efficiency to recover periodically expressed genes. Based on in silico experiments for microarray measurements of Saccharomyces cerevisiae, Lomb-Scargle is found to be the most efficacious scheme. 149 genes are then identified to be periodically expressed in the Drosophila melanogaster data set. Springer 2008-06-04 /pmc/articles/PMC3171399/ /pubmed/18584052 http://dx.doi.org/10.1155/2008/769293 Text en Copyright © 2008 Wentao Zhao et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhao, Wentao
Agyepong, Kwadwo
Serpedin, Erchin
Dougherty, Edward R
Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title_full Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title_fullStr Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title_full_unstemmed Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title_short Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study
title_sort detecting periodic genes from irregularly sampled gene expressions: a comparison study
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171399/
https://www.ncbi.nlm.nih.gov/pubmed/18584052
http://dx.doi.org/10.1155/2008/769293
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