{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T16:15:53Z","timestamp":1714580153105},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: There is a substantial body of works in the biology literature that seeks to characterize the cyclic behavior of genes during cell division. Gene expression microarrays made it possible to measure the expression profiles of thousands of genes simultaneously in time-course experiments to assess changes in the expression levels of genes over time. In this context, the commonly used procedures for testing include the permutation test by de Lichtenberg et al. and the Fisher\u2019s G-test, both of which are designed to evaluate periodicity against noise. However, it is possible that a gene of interest may have expression that is neither cyclic nor just noise. Thus, there is a need for a new test for periodicity that can identify cyclic patterns against not only noise but also other non-cyclic patterns such as linear, quadratic or higher order polynomial patterns.<\/jats:p><jats:p>Results: To address this weakness, we have introduced an empirical Bayes approach to test for periodicity and compare its performance in terms of sensitivity and specificity with that of the permutation test and Fisher\u2019s G-test through extensive simulations and by application to a set of time-course experiments on the Schizosaccharomyces pombe cell-cycle gene expression. We use \u2018conserved\u2019 and \u2018cycling\u2019 genes by Lu et al. to assess the sensitivity and CESR genes by Chenet al. to assess the specificity of our new empirical Bayes method.<\/jats:p><jats:p>Availability and implementation: The SAS Macro for our empirical Bayes test for periodicity is included in the supplementary materials along with a sample run of the MACRO program.<\/jats:p><jats:p>Contact: \u00a0mkocak1@uthsc.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts672","type":"journal-article","created":{"date-parts":[[2012,11,21]],"date-time":"2012-11-21T01:49:46Z","timestamp":1353462586000},"page":"182-188","source":"Crossref","is-referenced-by-count":3,"title":["An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data"],"prefix":"10.1093","volume":"29","author":[{"given":"Mehmet","family":"Kocak","sequence":"first","affiliation":[{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"},{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Olusegun George","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saumyadipta","family":"Pyne","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"},{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stanley","family":"Pounds","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38105, USA, 2Department of Biostatistics, St Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA, 3Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152, USA, 4C.R. Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh 500046, India and 5Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,19]]},"reference":[{"key":"2023012810150369300_bts672-B1","first-page":"160","article-title":"Detecting the long term cyclical behaviour of the Turkish stock market by means of spectral analysis","volume":"67","author":"Akar","year":"2011","journal-title":"Int. Res. J Finance Econ."},{"key":"2023012810150369300_bts672-B2","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1287\/msom.1100.0308","article-title":"Achieving a long-term service target with periodic demand signals: a newsvendor framework","volume":"13","author":"Bensoussan","year":"2011","journal-title":"Manuf. Serv. Oper. 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