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	Nätverksbaserad analys av mikrobiomdiversitet	RNA-seq Differential Expression
Ämnesområde	Bioinformatik	Bioinformatik
Familj	Process / pipeline	Process / pipeline
Ursprungsår	2012	2008–2010 (RNA-seq DE methodology established)
Upphovsperson	Faust, Raes, Friedman, Alm and colleagues	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Typ	Integrative bioinformatics pipeline	Quantitative genomics pipeline
Ursprungskälla	Friedman, J., & Alm, E. J. (2012). Inferring correlation networks from genomic survey data. PLoS Computational Biology, 8(9), e1002687.	Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.
Alias	microbial co-occurrence network analysis, microbiome network ecology, ecological network-based diversity, NBMDA	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Närliggande	5	6
Sammanfattning	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.	RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values.