مقایسهٔ روش‌ها

	تحلیل eQTL با کمک یادگیری ماشین	تحلیل بیان افتراقی RNA-seq
حوزه	زیست‌اطلاعاتی	زیست‌اطلاعاتی
خانواده	Process / pipeline	Process / pipeline
سال پیدایش	2015 (key ML-eQTL methods; foundational eQTL work: Jansen & Nap 2001)	2008–2010 (RNA-seq DE methodology established)
پدیدآور	Gamazon et al. (PrediXcan), Zhou & Troyanskaya (DeepSEA); broader field ca. 2015-onward	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
نوع	Statistical-computational genomics pipeline	Quantitative genomics pipeline
منبع بنیادین	Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., ... & Im, H. K. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47(9), 1091-1098.	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	ML-assisted eQTL analysis, ML eQTL mapping, deep learning eQTL, predictive eQTL modeling	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
مرتبط	6	6
خلاصه	Machine learning-assisted eQTL analysis integrates supervised learning models — ranging from elastic-net regression to deep neural networks — into the classical eQTL framework to predict and map genetic variants that regulate gene expression. By training predictive models on reference panels (e.g., GTEx), the approach enables imputation of gene expression in cohorts lacking RNA data, substantially increasing statistical power and enabling trans-tissue generalisation.	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.