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bioRxiv · 10.64898/2026.10.09.757957

An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements

Jiang, X.·Fang, Y.·Fang, Q.·Zhang, S.·Li, G.·Xu, H.·Feng, C.·Chen, M.
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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/.

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Jiang, X., Fang, Y., Fang, Q., Zhang, S., Li, G., Xu, H., Feng, C., Chen, M.. 2026-10-15. An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements. https://doi.org/10.64898/2026.10.09.757957

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