方法对比

	基于网络的微生物组多样性分析	通路富集分析
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2012	2003–2005
提出者	Faust, Raes, Friedman, Alm and colleagues	Mootha et al. (2003); systematised by Subramanian et al. (2005)
类型	Integrative bioinformatics pipeline	Statistical functional annotation method
开创性文献	Friedman, J., & Alm, E. J. (2012). Inferring correlation networks from genomic survey data. PLoS Computational Biology, 8(9), e1002687.	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.
别名	microbial co-occurrence network analysis, microbiome network ecology, ecological network-based diversity, NBMDA	PEA, overrepresentation analysis, ORA, functional enrichment analysis
相关	5	6
摘要	Network-based microbiome diversity analysis integrates graph-theoretic co-occurrence network inference with classical alpha- and beta-diversity metrics to characterize the structural organization of microbial communities. Rather than treating taxa as independent entities, the method models pairwise microbial associations as edges in a network, enabling identification of keystone taxa, community modules, and ecological interaction patterns that simple diversity indices cannot detect.	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.