Methoden vergelijken

	Time-Series Pathway Enrichment Analysis	Differentiële expressieanalyse van tijdreeks-RNA-seq
Vakgebied	Bio-informatica	Bio-informatica
Familie	Process / pipeline	Process / pipeline
Jaar van ontstaan	2005–2014	2006–2018 (principal methods established)
Grondlegger	Bar-Joseph and colleagues (temporal gene expression); extended by Cheng, Bhatt et al. for pathway-level time-series inference	Conesa et al. (maSigPro, 2006); extended by Fischer et al. (ImpulseDE2, 2018) and others
Type	Functional enrichment analysis with temporal modeling	Computational genomics pipeline
Oorspronkelijke bron	Ernst, J., Nau, G. J., & Bar-Joseph, Z. (2005). Clustering short time series gene expression data. Bioinformatics, 21(Suppl 1), i159–i168.	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.
Aliassen	temporal pathway analysis, longitudinal pathway enrichment, dynamic pathway analysis, TPEA	longitudinal RNA-seq DE analysis, temporal transcriptomics, time-course RNA-seq, dynamic DE analysis
Verwant	5	6
Samenvatting	Time-series pathway enrichment analysis identifies biological pathways whose coordinated gene activity changes significantly across ordered time points. Rather than treating each time point independently, the method models the temporal trajectory of gene expression within each pathway and tests whether entire biological programs — not just individual genes — are activated or suppressed in a time-dependent manner. It is widely used in developmental biology, drug response studies, and infection time courses.	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.