Methoden vergleichen

	Differenzielle Expressionsanalyse von Einzelzell-RNA-seq	Pathway Enrichment Analysis
Fachgebiet	Bioinformatik	Bioinformatik
Familie	Process / pipeline	Process / pipeline
Entstehungsjahr	2013–2015 (first scRNA-seq DE tools; refined 2015–present)	2003–2005
Urheber	Pioneered through Seurat (Satija lab) and scde (Kharchenko lab) frameworks, building on bulk RNA-seq DE foundations	Mootha et al. (2003); systematised by Subramanian et al. (2005)
Typ	Computational bioinformatics pipeline	Statistical functional annotation method
Wegweisende Quelle	Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology, 36(5), 411–420.	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	scRNA-seq DE, single-cell differential expression, scDE, cell-level differential expression analysis	PEA, overrepresentation analysis, ORA, functional enrichment analysis
Verwandt	5	6
Zusammenfassung	Single-cell RNA-seq differential expression (scRNA-seq DE) analysis identifies genes whose expression levels differ significantly between defined groups of individual cells — such as cell types, disease states, or treatment conditions. Unlike bulk RNA-seq, which averages signals across millions of cells, scRNA-seq DE operates on the transcriptome of each individual cell, enabling fine-grained characterization of cell-population-specific gene regulation and heterogeneity within seemingly homogeneous tissue.	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.