Detecting periodic genes from irregularly sampled gene expressions

A comparison study

Erchin Serpedin, Wentao Zhao, Kwadwo Agyepong, Edward R. Dougherty

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number769293
JournalEurasip Journal on Bioinformatics and Systems Biology
Volume2008
DOIs
Publication statusPublished - 2008
Externally publishedYes

Fingerprint

Microarrays
Gene expression
Microarray
Gene Expression
Genes
Gene
Irregular Sampling
Drosophilidae
Cell Cycle
Saccharomyces Cerevisiae
Spectral Analysis
Drosophila melanogaster
Missing Data
Computer Simulation
Yeast
Spectrum analysis
Saccharomyces cerevisiae
Time series
Cells
Sampling

ASJC Scopus subject areas

  • Signal Processing
  • Statistics and Probability
  • Computer Science(all)
  • Medicine(all)
  • General

Cite this

Detecting periodic genes from irregularly sampled gene expressions : A comparison study. / Serpedin, Erchin; Zhao, Wentao; Agyepong, Kwadwo; Dougherty, Edward R.

In: Eurasip Journal on Bioinformatics and Systems Biology, Vol. 2008, 769293, 2008.

Research output: Contribution to journalArticle

@article{972c2ac166b7494bb106b69e79201306,
title = "Detecting periodic genes from irregularly sampled gene expressions: A comparison study",
abstract = "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.",
author = "Erchin Serpedin and Wentao Zhao and Kwadwo Agyepong and Dougherty, {Edward R.}",
year = "2008",
doi = "10.1155/2008/769293",
language = "English",
volume = "2008",
journal = "Eurasip Journal on Bioinformatics and Systems Biology",
issn = "1687-4145",
publisher = "Springer Publishing Company",

}

TY - JOUR

T1 - Detecting periodic genes from irregularly sampled gene expressions

T2 - A comparison study

AU - Serpedin, Erchin

AU - Zhao, Wentao

AU - Agyepong, Kwadwo

AU - Dougherty, Edward R.

PY - 2008

Y1 - 2008

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=47649126156&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=47649126156&partnerID=8YFLogxK

U2 - 10.1155/2008/769293

DO - 10.1155/2008/769293

M3 - Article

VL - 2008

JO - Eurasip Journal on Bioinformatics and Systems Biology

JF - Eurasip Journal on Bioinformatics and Systems Biology

SN - 1687-4145

M1 - 769293

ER -