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Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis

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Abstract

A circadian rhythm is a roughly 24-h cycle in biological processes and physiological phenomena such as sleep, feeding, and photosynthesis for many organisms on Earth. The circadian patterns are coordinated by rhythmical gene expression of clock genes. Time-course transcriptomic analyses involving statistical methods have shown coordination of periodic gene expression in many organisms. Here we applied the cosine fitting method COSOPT to identify novel oscillating genes in microarray data for the chordate Ciona intestinalis. This organism showed rhythmic oxygen consumption in our previous study, but there were few homologous clock genes showing rhythmic mRNA expression. To understand circadian behavior at the transcriptomic level, we analyzed the 817 of 21,938 probes showing a 23- to 25-h period by means of COSOPT. Coupling the analysis of period detection with functional annotations indicated that previously unknown rhythmic mRNA expression might exist in C. intestinalis. In addition, we are releasing our implementation of COSOPT by means of R and C. All source code and supplementary information are available from https://github.com/mhiromi/cosopt.

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Author notes

  1. Hiromi Matsumae

    Present address: Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland

  2. Ryosuke Ishiwata

    Present address: Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, 4648601, Japan

Authors and Affiliations

  1. Department of Bioinformatics, Tokyo Medical and Dental University, Tokyo, Japan

    Hiromi Matsumae, Ryosuke Ishiwata & Hiroshi Tanaka

  2. Graduate School of Human Development and Environment, Kobe University, Kobe, Japan

    Toshifumi Minamoto

  3. Ishida Gr. of Clock Gene, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan

    Norio Ishida

  4. Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan

    Norio Ishida

  5. Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan

    Soichi Ogishima & Hiroshi Tanaka

Authors
  1. Hiromi Matsumae
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  2. Ryosuke Ishiwata
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  3. Toshifumi Minamoto
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  4. Norio Ishida
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  5. Soichi Ogishima
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  6. Hiroshi Tanaka
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Corresponding author

Correspondence to Hiromi Matsumae.

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Matsumae, H., Ishiwata, R., Minamoto, T. et al. Detection of periodic patterns in microarray data reveals novel oscillating transcripts of biological rhythms in Ciona intestinalis . Artif Life Robotics 20, 347–352 (2015). https://doi.org/10.1007/s10015-015-0237-6

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  • DOI: https://doi.org/10.1007/s10015-015-0237-6

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