GTEx pro enables accurate multi-tissue gene expression analysis using robust normalization and batch correction

Abstract

Abstract The Genotype-Tissue Expression (GTEx) project provides a valuable resource for investigating gene regulation across various human tissues. However, its cross-sectional design introduces technical artifacts and batch effects related to donor demographics and tissue processing. These confounders obscure biological signals and distort multi-tissue analyses. We present GTEx_Pro, a Nextflow-based pipeline for preprocessing GTEx v8 transcriptomic data, enhancing multi-tissue comparability. It integrates TMM + CPM normalization and SVA batch effect correction to improve biological signal recovery while reducing systematic variations across 54 GTEx tissues. Designed for scalability and reproducibility, GTEx_Pro facilitates accurate multi-tissue transcriptomic analysis, and a similar framework can be adapted to other large-scale transcriptome datasets.