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The cyclohedron test for finding periodic genes in time course expression studies
Jason Morton1, Lior Pachter, Anne Shiu
1University of California, Berkeley, CA, USA. mortonj@math.berkeley.edu
Statistical Applications in Genetics and Molecular Biology
|September 4, 2007
Summary
We developed a new statistical test, the cyclohedron test, to identify genes with periodic expression patterns in biological clock research. This method successfully found 32 significant periodic genes during mouse somitogenesis.
Area of Science:
- Genomics
- Systems Biology
- Bioinformatics
Background:
- Identifying genes with periodic expression is crucial for understanding biological clocks.
- Time course microarray experiments are widely used to study gene expression dynamics.
Purpose of the Study:
- To introduce a novel statistical approach, the cyclohedron test, for detecting periodically expressed genes.
- To apply this test to mouse somitogenesis data and identify novel candidate genes involved in the segmentation clock.
Main Methods:
- Utilized the cyclohedron test, a rank-based statistical method derived from algebraic combinatorics.
- Applied the test to time course gene expression data from mouse somitogenesis.
- Implemented the test within a multiple testing framework to ascertain statistical significance.
Main Results:
- Identified 32 genes with statistically significant periodic expression during mouse somitogenesis.
- Confirmed known periodic genes involved in Notch/FGF and Wnt signaling pathways.
- Discovered novel candidate genes potentially regulating the segmentation clock.
Conclusions:
- The cyclohedron test is a robust and effective method for identifying periodic genes from time course expression data.
- Somitogenesis involves a substantial number of highly periodic genes, including known and novel candidates.
- This approach enhances the analysis of biological clock mechanisms through advanced statistical and combinatorial methods.
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