ArticleBioinformatics (Oxford, England)2022
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Review
- Diving Deeper Into Mechanisms of Acrylamide-Induced Toxicity: RNA Sequencing Reveals Transcriptomic Alteration and Retrotransposon Expression in Drosophila melanogaster.Environmental toxicology · 2026Article
- Differential gene expression of retrotransposons (LTR and non-LTR) in peripheral blood leukocytes of people with gout.Arthritis research & therapy · 2026Article
- Sex-biased Expression of Genes and Transposable Elements in Hybrids from Drosophila mojavensis and Drosophila arizonae.Genome biology and evolution · 2026Article
- Characterization of the transposable element landscape shaping the Ectocarpus genome.Genome biology · 2025Article
- DNA hypomethylation traits define human regulatory T cells in cutaneous tissue and identify their blood recirculating counterparts.Nature immunology · 2025Article
- From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Drought-induced transposon expression reveals complex drought response mechanisms inFrontiers in plant science · 2025Article
- MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data.Frontiers in bioinformatics · 2025Article
- Transcription of endogenous retroviruses in senescent cells contributes to the accumulation of double-stranded RNAs that trigger an anti-viral response that reinforces senescence.Cell death & disease · 2024Article
- Towards targeting transposable elements for cancer therapy.Nature reviews. Cancer · 2024Review
- Transposon dynamics in the emerging oilseed crop Thlaspi arvense.PLoS genetics · 2024Article
- LINE-1 regulates cortical development by acting as long non-coding RNAs.Nature communications · 2023Article
- Exploratory analysis of L1 retrotransposons expression in autism.Molecular autism · 2023Article
- Article
- Transposons Acting as Competitive Endogenous RNAs: In-Silico Evidence from Datasets Characterised by L1 Overexpression.Biomedicines · 2022Article
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5 authors.
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Abstract
summaryTransposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. AVAILABILITY AND IMPLEMENTATION: The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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