Linganisha mbinu

	Utafiti wa Ulinganifu wa Epigenome kwa Njia ya Multi-Omics	Uchanganuzi wa Uboreshaji wa Njia
Nyanja	Bioinformatiki	Bioinformatiki
Familia	Process / pipeline	Process / pipeline
Mwaka wa asili	2011 (EWAS foundation); multi-omics integration ~2015–2020	2003–2005
Mwanzilishi	Rakyan, Down, Balding & Beck (EWAS framework); multi-omics integration extended by multiple groups (~2015–2020)	Mootha et al. (2003); systematised by Subramanian et al. (2005)
Aina	Integrative association study	Statistical functional annotation method
Chanzo asilia	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.
Majina mbadala	multi-omics EWAS, integrative EWAS, multi-layer epigenome-wide association, multi-omics epigenomic integration	PEA, overrepresentation analysis, ORA, functional enrichment analysis
Zinazohusiana	4	6
Muhtasari	A multi-omics epigenome-wide association study (multi-omics EWAS) systematically scans the entire epigenome — typically DNA methylation at CpG sites — for associations with a phenotype of interest, then integrates findings across additional omics layers such as transcriptomics, genomics, proteomics, or metabolomics. By linking epigenetic variation to molecular changes at multiple biological levels simultaneously, this approach identifies regulatory mechanisms and biomarkers that single-omics EWAS cannot resolve.	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.