مقایسهٔ روش‌ها

	تحلیل مبتنی بر شبکه برای نقاط کمی بیان ژن	تحلیل بیان افتراقی RNA-seq
حوزه	زیست‌اطلاعاتی	زیست‌اطلاعاتی
خانواده	Process / pipeline	Process / pipeline
سال پیدایش	2008–2013 (network-integrated extensions of eQTL mapping)	2008–2010 (RNA-seq DE methodology established)
پدیدآور	Multiple groups; foundational eQTL work by Cheung et al. (2005) and Stranger et al. (2007); network integration extended by Zhu et al. (2008) and others	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
نوع	Statistical genomics / network analysis pipeline	Quantitative genomics pipeline
منبع بنیادین	Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., & Holmes, I. H. (2009). JBrowse: a next-generation genome browser. Genome Research, 19(9), 1630–1638.	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.
نام‌های دیگر	network eQTL, network-integrated eQTL mapping, graph-based eQTL analysis, eQTL network analysis	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
مرتبط	5	6
خلاصه	Network-based eQTL analysis extends classical eQTL mapping by embedding genetic variant-to-expression associations within gene regulatory or protein interaction networks. Rather than treating each SNP-gene pair independently, this approach leverages network topology — such as co-expression modules or known pathway structures — to improve statistical power, reduce multiple testing burden, and reveal how genetic variants perturb entire regulatory programs rather than isolated transcripts.	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.