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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell

Xini Meng1,2,3, Zhi Nie1,2,3,4, Qifei Wang1,2,3

  • 1China National Center for Bioinformation, Beijing 100101, China.

Nucleic Acids Research
|November 26, 2025
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Summary
This summary is machine-generated.

Transposable elements (TEs), often silenced, can drive cancer when dysregulated. TE-SCALE is a new database enabling single-cell analysis of TE expression across human cancers, aiding biomarker discovery.

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Area of Science:

  • Genomics
  • Cancer Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are repetitive DNA sequences crucial in genome evolution.
  • TE dysregulation is implicated in cancer development, affecting oncogene activation.
  • Existing single-cell analyses often omit TEs due to their repetitive nature, limiting comprehensive cancer research.

Purpose of the Study:

  • To develop a systematic resource for exploring single-cell transposable element dynamics in human cancers.
  • To create a comprehensive database for integrative analysis and visualization of TE expression across diverse cancer types.
  • To facilitate the identification of novel TE-based biomarkers for cancer diagnosis and treatment.

Main Methods:

  • Development of the scTEfinder pipeline for single-cell TE quantification.
  • Integration of over 1.3 million cells from 330 samples across 20 cancer types into the TE-SCALE database.
  • Implementation of analytical modules for differential TE expression, TE-gene co-expression network analysis, and functional enrichment.

Main Results:

  • TE-SCALE provides a pan-cancer TE expression atlas with multi-scale exploration capabilities.
  • The database enables identification of tumor-specific TEs with potential clinical applications.
  • User-friendly web interface facilitates browsing, searching, analysis, and data download.

Conclusions:

  • TE-SCALE is a valuable resource for understanding TE biology in cancer.
  • The platform aids in decoding the role of TEs in tumorigenesis and cancer progression.
  • TE-SCALE accelerates the translation of TE research into clinical applications, including biomarker discovery and immunotherapeutic targeting.