Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach.
Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach.
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DOI：
10.1089/omi.2010.0074
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发表时间：
2011-01
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通讯作者：
Hiroki Takahashi;R. Morioka;Ryosuke Ito;T. Oshima;M. Altaf-Ul-Amin;N. Ogasawara;S. Kanaya
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文献类型：
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作者：
Hiroki Takahashi;R. Morioka;Ryosuke Ito;T. Oshima;M. Altaf-Ul-Amin;N. Ogasawara;S. Kanaya
在后基因组学时代，要把细胞作为一个系统来理解，就必须对多个“组学”数据进行综合分析。转录组学和代谢组学的综合分析可以导致基因代谢网络的阐明。在整合不同的时间序列“组学”数据时，有必要考虑到这些数据之间的时滞。在本研究中，我们进行了整合分析的时间序列转录组学和代谢组学数据的大肠杆菌的cDNA微阵列和傅立叶变换离子回旋共振质谱（FT-ICR/MS），分别。我们通过使用线性动力学系统确定了转录组学和代谢组学数据的转换点之间的60分钟时滞。此外，我们研究了基因与代谢物的相关性的背景下的时间滞后，获得了最大数量的相关对在成绩单导致60分钟的时间滞后，并最终揭示了基因代谢物的磷脂生物合成途径中的关系。考虑到时间序列分析中转录组学和代谢组学数据之间的时间滞后，可以揭示新的基因与代谢物的关系。根据基因与代谢产物的相关性，磷脂酰甘油在E.杆菌
In the postgenomics era, integrative analysis of several "omics" data is absolutely required for understanding the cell as a system. Integrative analysis of transcriptomics and metabolomics can lead to elucidation of gene-to-metabolite networks. When integrating different time series "omics" data, it is necessary to take into consideration a time lag between those data. In the present study, we conducted an integrative analysis of time series transcriptomics and metabolomics data of Escherichia coli generated by cDNA microarray and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS), respectively. We identified a 60-min time lag between transition points of transcriptomics and metabolomics data by using a Linear Dynamical System. Furthermore, we investigated gene-to-metabolite correlations in the context of time lag, obtained the maximum number of correlated pairs at transcripts leading 60-min time lag, and finally revealed gene-to-metabolite relations in the phospholipid biosynthesis pathway. Taking into consideration the time lag between transcriptomics and metabolomics data in time series analysis could unravel novel gene-to-metabolite relations. According to gene-to-metabolite correlations, phosphatidylglycerol plays a more critical role for membrane balance than phosphatidylethanolamine in E. coli.