مقایسهٔ روش‌ها

	تجزیه و تحلیل توالی‌یابی RNA تک‌سلولی	Pathway Enrichment Analysis
حوزه	زیست‌اطلاعاتی	زیست‌اطلاعاتی
خانواده	Process / pipeline	Process / pipeline
سال پیدایش	2009 (first scRNA-seq by Tang et al.); widely adopted 2015–2016	2003–2005
پدیدآور	Azim Surani, Barbara Treutlein, and the Regev/McCarroll groups (foundational droplet-based methods ~2015)	Mootha et al. (2003); systematised by Subramanian et al. (2005)
نوع	High-throughput single-cell transcriptomic profiling pipeline	Statistical functional annotation method
منبع بنیادین	Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33(5), 495–502.	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.
نام‌های دیگر	scRNA-seq, single-cell transcriptomics, scRNAseq analysis, single-cell gene expression profiling	PEA, overrepresentation analysis, ORA, functional enrichment analysis
مرتبط	5	6
خلاصه	Single-cell RNA sequencing (scRNA-seq) analysis characterises gene expression at the resolution of individual cells, enabling discovery of cell types, states, and transitions that are invisible in bulk transcriptomics. Starting from raw sequencing reads, the workflow produces a cell-by-gene count matrix and proceeds through quality control, normalisation, dimensionality reduction, unsupervised clustering, cell-type annotation, and a range of downstream analyses such as trajectory inference and differential expression between cell populations.	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.