title: Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach.
abstract: 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.
authors.affiliation: Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Nara, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Ryoko
authors.initials: R
authors.lastname: Morioka
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Ito
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.forename: Naotake
authors.initials: N
authors.lastname: Ogasawara
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D005583:Fourier Analysis; D020869:Gene Expression Profiling; D013058:Mass Spectrometry; D055432:Metabolomics; D020411:Oligonucleotide Array Sequence Analysis; D017550:Spectroscopy, Fourier Transform Infrared