A network biology study on circadian rhythm by integrating various omics data.
作者： Yong Wang , Xiang-Sun Zhang , Luonan Chen
关键词: Gene expression profiling 、 Suprachiasmatic nucleus 、 Mechanism (biology) 、 Circadian rhythm 、 Bacterial circadian rhythms 、 Genetics 、 Biology 、 Biological network 、 Regulation of gene expression 、 Computational biology 、 Gene regulatory network
摘要: Abstract Circadian rhythm is fundamentally important in physiological processes of mammals. To reveal its underlying mechanism, we probed functional interactions among genes, motivated by the basic molecular observation on gene expression data circadian that a large number genes oscillate coordinated manner. In this study, reverse-engineering strategy was applied to infer and analyze structure function rhythm-related regulatory network. Specifically, our method integrated four phase-shift time-course datasets rat suprachiasmatic nucleus, protein–protein interactions, phosphorylations set key prior information cis-regulatory elements, construct network related rat. By follow-up analysis, identified new hubs may play crucial roles regulation rhythm. Furthermore, found feedback loop motifs were significantly en...
aporc.org参考文章(28)
Katsuhisa Horimoto, Hajime Tei, Masanori Arita, Soshi Kawaguchi, Katsuhiko Sakamoto, Ryoko Morioka, Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus ,(2008)
Rui-Sheng Wang, Luonan Chen, Xiang-Sun Zhang, Biomolecular Networks: Methods and Applications in Systems Biology ,(2009)
Bernhard O. Palsson, Systems Biology: Properties of Reconstructed Networks ,(2006)
Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, Supervised Inference of Gene Regulatory Networks by Linear Programming Computational Intelligence and Bioinformatics. pp. 551- 561 ,(2006) , 10.1007/11816102_59
Uri Alon, An Introduction to Systems Biology Chapman and Hall/CRC. ,(2006) , 10.1201/9781420011432
J. Tegner, M. K. S. Yeung, J. Hasty, J. J. Collins, Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling Proceedings of the National Academy of Sciences of the United States of America. ,vol. 100, pp. 5944- 5949 ,(2003) , 10.1073/PNAS.0933416100
MICHIEL J. L. DE HOON, SEIYA IMOTO, KAZUO KOBAYASHI, NAOTAKE OGASAWARA, SATORU MIYANO, Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. pacific symposium on biocomputing. pp. 17- 28 ,(2002) , 10.1142/9789812776303_0003
Hiroki R Ueda, Satoko Hayashi, Wenbin Chen, Motoaki Sano, Masayuki Machida, Yasufumi Shigeyoshi, Masamitsu Iino, Seiichi Hashimoto, System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nature Genetics. ,vol. 37, pp. 187- 192 ,(2005) , 10.1038/NG1504
Masuo Obinata, Kaoru Saigo, Yoshiyuki Sakaki, Hajime Tei, Soshi Kawaguchi, Atsuki Shinozaki, Establishment of cell lines derived from the rat suprachiasmatic nucleus. Biochemical and Biophysical Research Communications. ,vol. 355, pp. 555- 561 ,(2007) , 10.1016/J.BBRC.2007.02.009
Jun Yan, Haifang Wang, Yuting Liu, Chunxuan Shao, Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm PLoS Computational Biology. ,vol. 4, pp. e1000193- ,(2008) , 10.1371/JOURNAL.PCBI.1000193