方法对比

	时间序列代谢组学分析	时间序列 RNA-seq 差异表达
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2000s–2010s	2006–2018 (principal methods established)
提出者	Developed from general metabolomics workflows; longitudinal extensions pioneered by A. K. Smilde, R. Bino, and colleagues	Conesa et al. (maSigPro, 2006); extended by Fischer et al. (ImpulseDE2, 2018) and others
类型	Quantitative longitudinal omics pipeline	Computational genomics pipeline
开创性文献	Smilde, A. K., van der Werf, M. J., Bijlsma, S., van der Werff-van der Vat, B. J. C., & Jellema, R. H. (2005). Fusion of mass spectrometry-based metabolomics data. Analytical Chemistry, 77(20), 6729–6736.	Conesa, A., Nueda, M. J., Ferrer, A., & Talon, M. (2006). maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics, 22(9), 1096–1102.
别名	longitudinal metabolomics, dynamic metabolomics, temporal metabolome profiling, kinetic metabolomics	longitudinal RNA-seq DE analysis, temporal transcriptomics, time-course RNA-seq, dynamic DE analysis
相关	6	6
摘要	Time-series metabolomics analysis profiles small-molecule metabolites from biological samples collected at multiple, ordered time points, enabling researchers to capture the dynamic flux of metabolic pathways in response to stimuli, disease progression, drug treatment, or developmental change. By integrating longitudinal statistical models with standard metabolomics preprocessing, the approach goes beyond a static metabolic snapshot to reveal how, when, and in what sequence metabolic responses unfold.	Time-series RNA-seq differential expression analysis identifies genes whose expression levels change systematically across ordered time points — such as during development, disease progression, or response to a treatment. Unlike two-condition DE analysis, it explicitly models the temporal structure of the data, capturing dynamic gene expression trajectories rather than a single snapshot contrast. Tools such as maSigPro, ImpulseDE2, and splineTimeR have been developed specifically for this design.