TEDD: a comprehensive database for translation efficiency dynamics

Nucleic Acids Res. 2026 Jan 6;54(D1):D511-D521. doi: 10.1093/nar/gkaf1125.

ABSTRACT

Translation, a core process in central dogma, is essential for gene expression and determination of biological phenotypes. High-throughput RNA-seq, Ribo-seq, and RNC-seq have enabled large-scale measurement of translation efficiency dynamics, yet systematic quantification and integration of translation efficiency (TE), initiation efficiency (translation ratio, TR), and elongation speed (elongation velocity index, EVI) at both gene and transcript levels across diverse biological contexts remain limited, even though their context-specific regulation-together with associated UTR features-plays key roles in development, homeostasis, and disease. To address this gap, we present TEDD (https://ngdc.cncb.ac.cn/tedd), a comprehensive database for exploring human TE, TR, and EVI with a focus on regulatory 5'/3' UTR features. TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) covering 24 tissues/cell types, 74 cell lines, and 52 conditions. Metrics are calculated at both gene and transcript levels, paired with detailed UTR annotations for fine-grained investigation of translational regulation. With user-friendly browsing, search, and download functions, TEDD offers an integrated online platform for multi-dimensional comparisons across genes, transcripts, Kyoto Encyclopedia of Genes and Genomes/Gene Ontology-defined gene sets, and UTR elements, providing a valuable resource for studying translational control and supporting basic and translational applications in messenger RNA vaccine design, synthetic biology, gene therapy, and enzyme engineering.

PMID:41217970 | PMC:PMC12807600 | DOI:10.1093/nar/gkaf1125