手法を比較

	ネットワークベースの遺伝子セット濃縮分析	経路濃縮解析
分野	バイオインフォマティクス	バイオインフォマティクス
系統	Process / pipeline	Process / pipeline
提唱年	2010 (NetGSA); field consolidated 2010-2015	2003–2005
提唱者	Ali Shojaie & George Michailidis (NetGSA); broader network-propagation approaches by multiple groups (~2010-2015)	Mootha et al. (2003); systematised by Subramanian et al. (2005)
種類	Network-informed statistical enrichment test	Statistical functional annotation method
原典	Shojaie, A., & Michailidis, G. (2010). Network enrichment analysis in complex experiments. Statistical Applications in Genetics and Molecular Biology, 9(1), Article 22.	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.
別名	network GSEA, network-propagation GSEA, NetGSA, graph-informed gene set testing	PEA, overrepresentation analysis, ORA, functional enrichment analysis
関連	5	6
概要	Network-based gene set enrichment analysis (network GSEA) extends classical GSEA by incorporating biological interaction networks — such as protein-protein interaction (PPI) or co-expression graphs — into the enrichment test. Instead of treating each gene independently, the method propagates differential expression signals across network edges, allowing genes that are co-regulated or functionally connected to jointly support the significance of a gene set. The result is a biologically coherent enrichment score that accounts for pathway topology and gene-gene dependencies.	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.