مقایسهٔ روش‌ها

	مطالعه انجمنی اپی‌ژِنوم-گسترده (EWAS)	Pathway Enrichment Analysis
حوزه	زیست‌اطلاعاتی	زیست‌اطلاعاتی
خانواده	Process / pipeline	Process / pipeline
سال پیدایش	2008–2011 (term and framework established c. 2011)	2003–2005
پدیدآور	Rakyan, Down, Balding & Beck (conceptual framework); Illumina arrays enabled large-scale application	Mootha et al. (2003); systematised by Subramanian et al. (2005)
نوع	Population-scale epigenomic association study	Statistical functional annotation method
منبع بنیادین	Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. (2011). Epigenome-wide association studies for common human diseases. Nature Reviews Genetics, 12(8), 529–541.	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	EWAS, methylome-wide association study, epigenetic association study, DNA methylation association study	PEA, overrepresentation analysis, ORA, functional enrichment analysis
مرتبط	5	6
خلاصه	An epigenome-wide association study (EWAS) is a hypothesis-free, genome-scale method that systematically tests whether epigenetic marks — predominantly CpG-site DNA methylation — differ between individuals with and without a trait, disease, or exposure. By scanning hundreds of thousands of genomic positions simultaneously, EWAS identifies loci where the epigenome is reproducibly associated with a phenotype, offering a layer of biological regulation that classical GWAS does not capture.	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.