Linganisha mbinu

	Utafiti wa Ulinganifu wa Epigenome kwa Msingi wa Mtandao (Network EWAS)	Uchambuzi wa Utekelezaji Tofauti wa RNA-seq
Nyanja	Bioinformatiki	Bioinformatiki
Familia	Process / pipeline	Process / pipeline
Mwaka wa asili	2010s, consolidating 2012–2018	2008–2010 (RNA-seq DE methodology established)
Mwanzilishi	Adapted from EWAS (Rakyan et al., 2011) and network-based genomic methods (e.g., Ideker & Sharan, 2008)	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Aina	Integrative epigenomic analysis	Quantitative genomics pipeline
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.	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.
Majina mbadala	network EWAS, network-integrated EWAS, graph-based EWAS, network-based DNA methylation analysis	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Zinazohusiana	6	6
Muhtasari	Network-based EWAS extends conventional epigenome-wide association studies by overlaying differentially methylated positions or regions onto biological interaction networks — such as protein-protein interaction, co-expression, or gene regulatory networks — to identify functionally coherent epigenetic modules rather than isolated CpG hits. This integration increases statistical power for detecting weak signals and reveals coordinated epigenetic dysregulation across pathways.	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.