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bioRxiv · 10.1101/2025.05.19.654796

TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers

Zhang, Y.·She, J.·Hu, X.·Jin, Y.·Tao, C.·Du, M.·Yang, E.
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Abstract

Transposable elements (TEs) are abundant and play a crucial regulatory role in the human genome. Functioning as alternative promoters, TEs can be reactivated to produce TE-initiated transcripts. In cancer, TE-initiated transcription may upregulate oncogene expression and generate novel tumor-specific antigens, which could serve as potential targets for immunotherapy. However, there remains a lack of comprehensive databases that systematically investigate TE-initiated transcription in cancer. To address this gap, we developed a deep learning-based method and identified 38,995 TE-initiated transcripts across 33 cancer types from The Cancer Genome Atlas. Among these, 6,203 were tumor-specific expressed and strongly associated with the tumorigenesis. Using these annotations, we created TEITbase (http://teitbase.medbioinfo.org/), a user-friendly database that provides researchers with tools to conduct various downstream analyses and investigations for TE-initiated transcripts, including 546 novel onco-exaptation events. The establishment of TEITbase provides new insights into transcriptional reprogramming in cancers and enables further investigation into the potential roles of TE-initiated transcripts in cancer diagnostics and therapeutic strategies.

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Zhang, Y., She, J., Hu, X., Jin, Y., Tao, C., Du, M., Yang, E.. 2025-05-23. TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers. https://doi.org/10.1101/2025.05.19.654796

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