title: The cyclohedron test for finding periodic genes in time course expression studies.
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.
authors.affiliation: University of California, Berkeley, CA, USA. mortonj@math.berkeley.edu
authors.forename: Jason
authors.initials: J
authors.lastname: Morton
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.forename: Anne
authors.initials: A
authors.lastname: Shiu
authors.forename: Bernd
authors.initials: B
authors.lastname: Sturmfels
mesh_terms: D000465:Algorithms; D000818:Animals; D001683:Biological Clocks / Q000502:physiology*; D002940:Circadian Rhythm / Q000502:physiology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D016695:Glycosyltransferases / Q000502:physiology*; D051379:Mice; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D013996:Time and Motion Studies
chemical_list: D016695:Glycosyltransferases; C498392:Lfng protein, mouse