TY - GEN
T1 - Identification and modeling of co-rhythmic genes from micro-array time series data
AU - Wang, Wenxue
AU - Ghosh, Bijoy
N1 - Funding Information:
This work is part of a Membrane Biology EMSL Scientific Grand Challenge project at the W. R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research (BER) program located at Pacific Northwest National Laboratory. PNNL is operated for the Department of Energy by Battelle. This work was also partially supported by funding from the NSF-FIBR program (EF0425749).
PY - 2008
Y1 - 2008
N2 - "Circadian Rhythm" is a biological phenomenon observed in a large number of organisms ranging from unicellular bacteria to human beings. In this paper, transcriptome data from Cyanothece, a photosynthetic cyanobacteria, has been analyzed for the purpose of discovering genes whose expressions are rhythmically close (co-rhythmic). Subsequently we study if these rhythms can be modeled, up to phase, using a cascade of three phase oscillators. One of the phase oscillator in the network is derived from the model of a "limit cycle oscillator" using KaiC protein (the master clock). We conclude that "Circadian Rhythms in Cyanothece transcriptome data can be dynamically modeled up to phase using a single master clock derived from limit cycle oscillator using KaiC protein cascaded with a pair of interconnected phase oscillators". Biologically substrates of the phase oscillators are presently unknown.
AB - "Circadian Rhythm" is a biological phenomenon observed in a large number of organisms ranging from unicellular bacteria to human beings. In this paper, transcriptome data from Cyanothece, a photosynthetic cyanobacteria, has been analyzed for the purpose of discovering genes whose expressions are rhythmically close (co-rhythmic). Subsequently we study if these rhythms can be modeled, up to phase, using a cascade of three phase oscillators. One of the phase oscillator in the network is derived from the model of a "limit cycle oscillator" using KaiC protein (the master clock). We conclude that "Circadian Rhythms in Cyanothece transcriptome data can be dynamically modeled up to phase using a single master clock derived from limit cycle oscillator using KaiC protein cascaded with a pair of interconnected phase oscillators". Biologically substrates of the phase oscillators are presently unknown.
KW - Bioinformatics
KW - Dynamics and control
KW - Modelling and identification
UR - http://www.scopus.com/inward/record.url?scp=79961018312&partnerID=8YFLogxK
U2 - 10.3182/20080706-5-KR-1001.2495
DO - 10.3182/20080706-5-KR-1001.2495
M3 - Conference contribution
AN - SCOPUS:79961018312
SN - 9783902661005
T3 - IFAC Proceedings Volumes (IFAC-PapersOnline)
BT - Proceedings of the 17th World Congress, International Federation of Automatic Control, IFAC
T2 - 17th World Congress, International Federation of Automatic Control, IFAC
Y2 - 6 July 2008 through 11 July 2008
ER -