Artificial Life and Robotics

, Volume 20, Issue 4, pp 347–352 | Cite as

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

  • Hiromi Matsumae
  • Ryosuke Ishiwata
  • Toshifumi Minamoto
  • Norio Ishida
  • Soichi Ogishima
  • Hiroshi Tanaka
Original Article

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.

Keywords

Ciona intestinalis Circadian rhythms COSOPT Microarray Time-series data analysis Transcriptome analysis 

Supplementary material

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Copyright information

© ISAROB 2015

Authors and Affiliations

  • Hiromi Matsumae
    • 1
    • 2
  • Ryosuke Ishiwata
    • 1
    • 3
  • Toshifumi Minamoto
    • 4
  • Norio Ishida
    • 5
    • 6
  • Soichi Ogishima
    • 7
  • Hiroshi Tanaka
    • 1
    • 7
  1. 1.Department of BioinformaticsTokyo Medical and Dental UniversityTokyoJapan
  2. 2.Institute of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
  3. 3.Department of Complex Systems Science, Graduate School of Information ScienceNagoya UniversityNagoyaJapan
  4. 4.Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
  5. 5.Ishida Gr. of Clock GeneNational Institute of Advanced Industrial Science and TechnologyTsukubaJapan
  6. 6.Graduate School of Life and Environmental SciencesUniversity of TsukubaTsukubaJapan
  7. 7.Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan

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