TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

Gökhan Karakülah; Nazmiye Arslan; Cihangir Yandım; Aslı Suner

doi:10.7717/peerj.8192

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

PeerJ. 2019 Dec 5:7:e8192. doi: 10.7717/peerj.8192. eCollection 2019.

Authors

Gökhan Karakülah^{1

2}, Nazmiye Arslan¹, Cihangir Yandım^{1

3}, Aslı Suner⁴

Affiliations

¹ Izmir Biomedicine and Genome Center, Izmir, Turkey.
² Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey.
³ Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Izmir, Turkey.
⁴ Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey.

Abstract

Introduction: Recent 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.

Keywords: Gene expression; Linear model; R package; Regression; Gene regulation; Transposable elements.

Grants and funding

The authors received no funding for this work.