방법 비교

	기계 학습 보조 eQTL 분석	RNA-seq 차등 발현
분야	생물정보학	생물정보학
계열	Process / pipeline	Process / pipeline
기원 연도	2015 (key ML-eQTL methods; foundational eQTL work: Jansen & Nap 2001)	2008–2010 (RNA-seq DE methodology established)
창시자	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)
유형	Statistical-computational genomics pipeline	Quantitative genomics pipeline
원전	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.
별칭	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
관련	6	6
요약	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.