An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements
Journal:
bioRxiv
Published Date:
Oct 15, 2026
Abstract
Transposable elements (TEs) constitute a substantial fraction of the human genome and contribute to genomic and epigenomic regulation. However, TE-related knowledge remains fragmented across the literature and databases, with inconsistent identifiers hindering integration and reuse. Here, we present TE-Dee (Transposable Element Data Exploration Engine), a curated resource that harmonizes literature-derived TE relationships with TE annotations, tissue-specific expression, and GTEx v11 eQTL associations. TE-Dee contains 10,387 entities and 9,583 curated relationships from 2,308 publications, 1,505 leaf-level TE classification records, and 11,334,060 instance-level observations generated by intersecting 640,456 reference TE intervals with significant variant-gene associations across 50 GTEx tissue categories. By linking molecular knowledge to genomic, transcriptomic and genetic evidence, TE-Dee provides reusable data for investigating TE biology, gene-regulatory and disease-related mechanisms, and a structured corpus for training and benchmarking data-driven and artificial intelligence models. TE-Dee is available at https://bis.zju.edu.cn/tedee/.
