ArticleBioinformatics (Oxford, England)2015
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 474 papers.
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Who cites it
474 citing papers in PubMed.
- Review
- Comprehensive characterization of transposable element expression reveals regulatory circuitry and clinical implications in cancers.Science advances · 2026Article
- Review
- Active and Unusually Expanded PIF/Harbinger Transposable Elements in the Caenorhabditis inopinata Genome.Genome biology and evolution · 2026Article
- Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- AcutebioRxiv : the preprint server for biology · 2026Article
- Updated guide to RNA quantification by RNA sequencing and reverse transcription-qPCR.Molecules and cells · 2026Article
- Activation of transposable elements is linked to a region- and cell type-specific interferon response in Parkinson's disease.Science advances · 2026Article
- The 3D genome of Gigaspora margarita unveils stable chromatin and nucleolar organization and symbiont-dependent genome dynamics.The New phytologist · 2026Article
- cGAS-deficient mice display premature aging associated with derepression of LINE1 elements and inflammation.Nature aging · 2026Article
- Mitochondrial DNA leakage in oocytes activates cGAS-STING signaling to drive ovarian aging.Nature aging · 2026Article
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Mutant TP53 hijacks RNA-splicing factor RBM28 to suppress double-stranded RNA triggered antitumor immunity.Nature communications · 2026Article
- Article
- Article
- Distinct endogenous retroviruses are expressed in mutational subtypes of clear cell renal cell carcinoma and are linked to improved clinical outcomes.Cell reports · 2026Article
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- DNA Hypomethylation Is Not Cell Intrinsically Toxic to Polycomb Repressive Complex 2 Deficient Malignant Peripheral Nerve Sheath Tumors.Genes, chromosomes & cancer · 2026Article
- SETDB1 modulates neuroinflammation in the mouse cortex by regulating neuronal P2rx7 expression.Molecular psychiatry · 2026Article
- Alterations in chromatin organization promote totipotent-like features in a DPPA2/DUX-dependent manner.The EMBO journal · 2026Article
414 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
motivationMost RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses.
resultsHere, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. AVAILABILITY AND IMPLEMENTATION: The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. CONTACT: mhammell@cshl.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.