Phase analysis of circadian-related genes in two tissues

BMC Bioinformatics
Delong LiuClarice R Weinberg

Abstract

Recent circadian clock studies using gene expression microarray in two different tissues of mouse have revealed not all circadian-related genes are synchronized in phase or peak expression times across tissues in vivo. Instead, some circadian-related genes may be delayed by 4-8 hrs in peak expression in one tissue relative to the other. These interesting biological observations prompt a statistical question regarding how to distinguish the synchronized genes from genes that are systematically lagged in phase/peak expression time across two tissues. We propose a set of techniques from circular statistics to analyze phase angles of circadian-related genes in two tissues. We first estimate the phases of a cycling gene separately in each tissue, which are then used to estimate the paired angular difference of the phase angles of the gene in the two tissues. These differences are modeled as a mixture of two von Mises distributions which enables us to cluster genes into two groups; one group having synchronized transcripts with the same phase in the two tissues, the other containing transcripts with a discrepancy in phase between the two tissues. For each cluster of genes we assess the association of phases across the tissue types us...Continue Reading

References

Apr 23, 2002·Nature·Kai-Florian StorchCharles J Weitz
May 23, 2002·Cell·Satchidananda PandaJohn B Hogenesch
Jun 12, 2002·Molecular Biology of the Cell·Michael L WhitfieldDavid Botstein
Aug 29, 2002·Nature·Steven M Reppert, David R Weaver
Nov 8, 2003·Science·Todd P MichaelC Robertson McClung
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Delong LiuClarice R Weinberg

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Citations

Jan 15, 2009·Neuroendocrinology·Sheng Zhao, Lance J Kriegsfeld
Dec 2, 2009·IET Systems Biology·R MoriokaK Horimoto
Jul 8, 2015·PloS One·Sandra BarragánShyamal D Peddada
May 1, 2015·Biochimie·Isabel MéndezMauricio Díaz-Muñoz
Jul 24, 2010·Journal of Neuroendocrinology·B L Conway-CampbellS L Lightman
Aug 19, 2007·Chronobiology International·Mamane SaniMossadok Ben-Attia
Apr 8, 2017·Oncotarget·Hiroaki HojoShinpei Kawaoka

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