Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. BMC Syst Biol 2010 Dec 03;4:167
Date
12/07/2010Pubmed ID
21129191Pubmed Central ID
PMC3017040DOI
10.1186/1752-0509-4-167Scopus ID
2-s2.0-78649564171 (requires institutional sign-in at Scopus site) 8 CitationsAbstract
BACKGROUND: In nonlinear dynamic systems, synchrony through oscillation and frequency modulation is a general control strategy to coordinate multiple modules in response to external signals. Conversely, the synchrony information can be utilized to infer interaction. Increasing evidence suggests that frequency modulation is also common in transcription regulation.
RESULTS: In this study, we investigate the potential of phase locking analysis, a technique to study the synchrony patterns, in the transcription network modeling of time course gene expression data. Using the yeast cell cycle data, we show that significant phase locking exists between transcription factors and their targets, between gene pairs with prior evidence of physical or genetic interactions, and among cell cycle genes. When compared with simple correlation we found that the phase locking metric can identify gene pairs that interact with each other more efficiently. In addition, it can automatically address issues of arbitrary time lags or different dynamic time scales in different genes, without the need for alignment. Interestingly, many of the phase locked gene pairs exhibit higher order than 1:1 locking, and significant phase lags with respect to each other. Based on these findings we propose a new phase locking metric for network reconstruction using time course gene expression data. We show that it is efficient at identifying network modules of focused biological themes that are important to cell cycle regulation.
CONCLUSIONS: Our result demonstrates the potential of phase locking analysis in transcription network modeling. It also suggests the importance of understanding the dynamics underlying the gene expression patterns.
Author List
Gao S, Hartman JL 4th, Carter JL, Hessner MJ, Wang XAuthor
Martin J. Hessner PhD Professor in the Pediatrics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Cell CycleGene Expression Profiling
Gene Regulatory Networks
Models, Genetic
Nonlinear Dynamics
Reproducibility of Results
Transcription Factors