مقایسهٔ روش‌ها

	تحلیل چند-اُمیکس eQTL	تحلیل بیان افتراقی RNA-seq
حوزه	زیست‌اطلاعاتی	زیست‌اطلاعاتی
خانواده	Process / pipeline	Process / pipeline
سال پیدایش	2010s–present (foundational eQTL work: ~2007; multi-omics integration: ~2013–2017)	2008–2010 (RNA-seq DE methodology established)
پدیدآور	GTEx Consortium and multi-omics integration pioneers (Nica & Dermitzakis, 2013; GTEx Consortium, 2015–2020)	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
نوع	Integrative genomic association analysis	Quantitative genomics pipeline
منبع بنیادین	GTEx Consortium. (2017). Genetic effects on gene expression across human tissues. Nature, 550(7675), 204–213.	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	multi-omics molQTL, multi-layer eQTL, integrated eQTL analysis, xQTL multi-omics	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
مرتبط	6	6
خلاصه	Multi-omics eQTL analysis maps genetic variants (SNPs or structural variants) to molecular phenotypes simultaneously across multiple omics layers — transcriptome, epigenome, proteome, and metabolome — in the same cohort. By linking genotype to gene expression and then tracing those effects through downstream molecular layers, the approach reveals how genetic variation propagates through the molecular machinery of a cell, yielding mechanistic insight that no single-omics eQTL study can provide.	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.