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The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies

Morton, Jason and Pachter, Lior and Shiu, Anne and Sturmfels, Bernd (2007) The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies. Statistical Applications in Genetics and Molecular Biology, 6 . Art. No. 21. ISSN 2194-6302. doi:10.2202/1544-6115.1286. https://resolver.caltech.edu/CaltechAUTHORS:20170306-154012533

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Abstract

The problem of finding periodically expressed genes from time course microarray experiments is at the center of numerous efforts to identify the molecular components of biological clocks. We present a new approach to this problem based on the cyclohedron test, which is a rank test inspired by recent advances in algebraic combinatorics. The test has the advantage of being robust to measurement errors, and can be used to ascertain the significance of top-ranked genes. We apply the test to recently published measurements of gene expression during mouse somitogenesis and find 32 genes that collectively are significant. Among these are previously identified periodic genes involved in the Notch/FGF and Wnt signaling pathways, as well as novel candidate genes that may play a role in regulating the segmentation clock. These results confirm that there are an abundance of exceptionally periodic genes expressed during somitogenesis. The emphasis of this paper is on the statistics and combinatorics that underlie the cyclohedron test and its implementation within a multiple testing framework.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.2202/1544-6115.1286DOIArticle
https://www.degruyter.com/view/j/sagmb.2007.6.issue-1/sagmb.2007.6.1.1286/sagmb.2007.6.1.1286.xmlPublisherArticle
https://arxiv.org/abs/q-bio/0702049arXivDiscussion Paper
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2007 by Walter de Gruyter GmbH. We are grateful to Mary-Lee Dequéant and Olivier Pourquié for many helpful discussions, and to Mary-Lee for preparing the data for our use. We thank Oliver Wienand for helping us implement the cyclohedron test. The collaboration was facilitated by the DARPA Fundamental Laws of Biology Program which supported our research. Anne Shiu was supported by a Lucent Technologies Bell Labs Graduate Research Fellowship. We thank an anonymous referee for helpful comments.
Funders:
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Lucent Technologies Bell LabsUNSPECIFIED
Subject Keywords:time course microarray; biological clock; somitogenesis; multiple testing
DOI:10.2202/1544-6115.1286
Record Number:CaltechAUTHORS:20170306-154012533
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170306-154012533
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74813
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Mar 2017 00:03
Last Modified:11 Nov 2021 05:30

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