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

Overview

Journal EURASIP J Bioinform Syst Biol

Publisher Springer

Specialty Biology

Date 2008 Jun 28

PMID 18584052

Citations 10

Authors

Wentao Zhao

Kwadwo Agyepong

Erchin Serpedin

Edward R Dougherty

Affiliations

Soon will be listed here.

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.

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References

de Lichtenberg U, Jensen L, Fausboll A, Jensen T, Bork P, Brunak S . Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics. 2004; 21(7):1164-71. DOI: 10.1093/bioinformatics/bti093. View

Ahdesmaki M, Lahdesmaki H, Pearson R, Huttunen H, Yli-Harja O . Robust detection of periodic time series measured from biological systems. BMC Bioinformatics. 2005; 6:117. PMC: 1168888. DOI: 10.1186/1471-2105-6-117. View

Ahdesmaki M, Lahdesmaki H, Gracey A, Shmulevich L, Yli-Harja O . Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. 2007; 8:233. PMC: 1934414. DOI: 10.1186/1471-2105-8-233. View

Luan Y, Li H . Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. Bioinformatics. 2004; 20(3):332-9. DOI: 10.1093/bioinformatics/btg413. View

Cooper S . Rethinking synchronization of mammalian cells for cell cycle analysis. Cell Mol Life Sci. 2003; 60(6):1099-106. PMC: 11138607. DOI: 10.1007/s00018-003-2253-2. View

Arbeitman M, Furlong E, Imam F, Johnson E, Null B, Baker B . Gene expression during the life cycle of Drosophila melanogaster. Science. 2002; 297(5590):2270-5. DOI: 10.1126/science.1072152. View

Reiter L, Potocki L, Chien S, Gribskov M, Bier E . A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster. Genome Res. 2001; 11(6):1114-25. PMC: 311089. DOI: 10.1101/gr.169101. View

Whitfield M, Sherlock G, Saldanha A, Murray J, Ball C, Alexander K . Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002; 13(6):1977-2000. PMC: 117619. DOI: 10.1091/mbc.02-02-0030. View

de Lichtenberg U, Wernersson R, Jensen T, Nielsen H, Fausboll A, Schmidt P . New weakly expressed cell cycle-regulated genes in yeast. Yeast. 2005; 22(15):1191-201. DOI: 10.1002/yea.1302. View

10.

Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M . Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998; 9(12):3273-97. PMC: 25624. DOI: 10.1091/mbc.9.12.3273. View

11.

Lu X, Zhang W, Qin Z, Kwast K, Liu J . Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic Acids Res. 2004; 32(2):447-55. PMC: 373332. DOI: 10.1093/nar/gkh205. View

12.

Wichert S, Fokianos K, Strimmer K . Identifying periodically expressed transcripts in microarray time series data. Bioinformatics. 2003; 20(1):5-20. DOI: 10.1093/bioinformatics/btg364. View

13.

Glynn E, Chen J, Mushegian A . Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics. 2005; 22(3):310-6. DOI: 10.1093/bioinformatics/bti789. View