TEDEdb: A multicohort analysis and resource for transposable element differential expression in cancer.

TEDEdb’s uniform reanalysis of over 7,000 RNA-seq samples across 220 cancer cell lines shows transposable element expression is more prone to batch effects than gene expression alone.

• Why it matters: Most RNA-seq analyses ignore transposable elements, leaving a large public dataset underused for studying how TE derepression relates to cancer and epigenetic therapy responses.
• What they did: The authors reanalyzed more than 2,000 differential expression experiments spanning 700 drug treatments, using meta-analysis to assess global trends and validate DNMTi/HDACi and nonepigenetic inducers.
• The result: DNMTi and HDACis robustly induce TE expression, and cyclin-dependent kinase and topoisomerase inhibitors also up-regulate TE-derived repetitive DNA linked to viral mimicry response signatures.