Methoden vergleichen

	Zeitreihen-Pathway-Analyse	Pathway Enrichment Analysis
Fachgebiet	Bioinformatik	Bioinformatik
Familie	Process / pipeline	Process / pipeline
Entstehungsjahr	2005–2014	2003–2005
Urheber	Bar-Joseph and colleagues (temporal gene expression); extended by Cheng, Bhatt et al. for pathway-level time-series inference	Mootha et al. (2003); systematised by Subramanian et al. (2005)
Typ	Functional enrichment analysis with temporal modeling	Statistical functional annotation method
Wegweisende Quelle	Ernst, J., Nau, G. J., & Bar-Joseph, Z. (2005). Clustering short time series gene expression data. Bioinformatics, 21(Suppl 1), i159–i168.	Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550.
Aliasnamen	temporal pathway analysis, longitudinal pathway enrichment, dynamic pathway analysis, TPEA	PEA, overrepresentation analysis, ORA, functional enrichment analysis
Verwandt	5	6
Zusammenfassung	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.	Pathway enrichment analysis (PEA) is a statistical approach that takes a list of genes or proteins of interest — typically derived from a differential expression or proteomics experiment — and identifies which pre-defined biological pathways or functional gene sets are represented more often than expected by chance. By mapping individual molecular changes onto curated pathway knowledge bases such as KEGG, Gene Ontology, or Reactome, PEA translates long gene lists into interpretable biological processes, making it a central tool in the post-analysis of high-throughput omics experiments.