An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements
- 1Zhejiang University
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/.
Related
- Transposable element DNA and RNA: Drivers of gene expression, evolution, and disease
- Transposable elements and the evolutionary origins of C4 gene expression: The story of carbonic anhydrases in Flaveria.
- Comprehensive characterization of transposable element expression reveals regulatory circuitry and clinical implications in cancers
- Transposable element-mediated structural variations shape gene expression and agronomic trait diversity in Brassica napus
- Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression
BibTeX
@misc{jiang2026integrated,
title = {{An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements}},
author = {X. Jiang and Y. Fang and Q. Fang and S. Zhang and G. Li and H. Xu and C. Feng and M. Chen},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.757957},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.757957v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements
AU - X. Jiang
AU - Y. Fang
AU - Q. Fang
AU - S. Zhang
AU - G. Li
AU - H. Xu
AU - C. Feng
AU - M. Chen
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.757957
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.757957v1
AB - 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/.
ER -