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

Karakulah G., Arslan N., Yandim C., SUNER KARAKÜLAH A.

PEERJ, vol.7, 2019 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 7
  • Publication Date: 2019
  • Doi Number: 10.7717/peerj.8192
  • Journal Name: PEERJ
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Keywords: Transposable elements, Gene regulation, Gene expression, Regression, Linear model, R package, IN-SITU, BREAST, DNA, TRANSCRIPTOME, MUTATION, CELLS, FEN1
  • Dokuz Eylül University Affiliated: Yes

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.