Methoden vergelijken

	eQTL-analyse	RNA-seq Differentiele Expressie
Vakgebied	Bio-informatica	Bio-informatica
Familie	Process / pipeline	Process / pipeline
Jaar van ontstaan	2001 (term coined); widely adopted after 2005	2008–2010 (RNA-seq DE methodology established)
Grondlegger	Ritsert C. Jansen & Jan-Peter Nap	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Type	Association mapping method	Quantitative genomics pipeline
Oorspronkelijke bron	Jansen, R. C., & Nap, J.-P. (2001). Genetical genomics: the added value from segregation. Trends in Genetics, 17(7), 388–391.	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.
Aliassen	eQTL mapping, expression QTL analysis, transcriptomic QTL analysis, eQTL study	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Verwant	6	6
Samenvatting	eQTL analysis identifies genomic loci (variants, typically SNPs) whose genotype statistically associates with variation in the expression level of one or more genes. By jointly profiling DNA-level variation and RNA-level expression in the same individuals, eQTL studies decode the regulatory grammar of the genome — revealing which variants control how much a gene is transcribed, in which tissues, and under what conditions.	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.