ArticlePeerJ2019
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Intermittent fasting rewires tissue-specific gene-transposable element regulatory networks.PNAS nexus · 2026Article
- TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model.Molecular genetics and genomics : MGG · 2026Article
- Article
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- PlanTEnrichment: A How-to Guide on Rapid Identification of Transposable Elements Associated with Regions of Interest in Select Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Activation of Transposable Elements in Human Skeletal Muscle Fibers upon Statin Treatment.International journal of molecular sciences · 2022Article
- Dysregulated Expression of Transposable Elements in TDP-43International journal of molecular sciences · 2022Article
- SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression.Communications biology · 2022Article
- Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements.Frontiers in genetics · 2022Review
- Differential regulation of transposable elements (TEs) during the murine submandibular gland development.Mobile DNA · 2021Article
- Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans.Mobile DNA · 2021Review
- Article
- Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.PloS one · 2021Article
- Measuring and interpreting transposable element expression.Nature reviews. Genetics · 2020Review
- Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence.Turkish journal of biology = Turk biyoloji dergisi · 2020Article
- Article
- Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer.PeerJ · 2020Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionRecent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE -proximal gene expression associations from RNA-sequencing data are still missing. IMPLEMENTATION: Herein, we developed a novel R package, using a linear regression model, for studying the potential influence of TE species on proximal gene expression from a given RNA-sequencing data set. Our R package, namely TEffectR, makes use of publicly available RepeatMasker TE and Ensembl gene annotations as well as several functions of other R-packages. It calculates total read counts of TEs from sorted and indexed genome aligned BAM files provided by the user, and determines statistically significant relations between TE expression and the transcription of nearby genes under diverse biological conditions. AVAILABILITY: TEffectR is freely available at https://github.com/karakulahg/TEffectR along with a handy tutorial as exemplified by the analysis of RNA-sequencing data including normal and tumour tissue specimens obtained from breast cancer patients.
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Registered trials
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.