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| Netzwerkbasierte Mikrobiom-Diversitätsanalyse× | RNA-seq Differential Expression× | |
|---|---|---|
| Fachgebiet | Bioinformatik | Bioinformatik |
| Familie | Process / pipeline | Process / pipeline |
| Entstehungsjahr≠ | 2012 | 2008–2010 (RNA-seq DE methodology established) |
| Urheber≠ | 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 |
| Wegweisende Quelle≠ | Friedman, J., & Alm, E. J. (2012). Inferring correlation networks from genomic survey data. PLoS Computational Biology, 8(9), e1002687. DOI ↗ | 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. DOI ↗ |
| Aliasnamen | 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 |
| Verwandt≠ | 5 | 6 |
| Zusammenfassung≠ | 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. |
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