Identification and modeling of genes with diurnal oscillations from microarray time series data.
Behavior of living organisms is strongly modulated by the day and night cycle giving rise to a cyclic pattern of activities. Such a pattern helps the organisms to coordinate their activities and maintain a balance between what could be performed during the "day" and what could be relegated to the "night." This cyclic pattern, called the "Circadian Rhythm," is a biological phenomenon observed in a large number of organisms. In this paper, our goal is to analyze transcriptome data from Cyanothece for the purpose of discovering genes whose expressions are rhythmic. We cluster these genes into groups that are close in terms of their phases and show that genes from a specific metabolic functional category are tightly clustered, indicating perhaps a "preferred time of the day/night" when the organism performs this function. The proposed analysis is applied to two sets of microarray experiments performed under varying incident light patterns. Subsequently, we propose a model with a network of three phase oscillators together with a central master clock and use it to approximate a set of "circadian-controlled genes" that can be approximated closely.
Institute for Collaborative Biotechnologies, University of California, Santa Barbara, 1223 Elings Hall, Santa Barbara, CA 93106-5100, USA. wenxue@engineering.ucsb.edu
Wenxue
W
Wang
Bijoy K
BK
Ghosh
Himadri B
HB
Pakrasi
D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics*; D056925:Circadian Rhythm Signaling Peptides and Proteins / Q000235:genetics / Q000502:physiology; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D046889:Cyanothece / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis
D001426:Bacterial Proteins; D056925:Circadian Rhythm Signaling Peptides and Proteins; C114271:KaiC protein, cyanobacteria