RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes


GENOMICS, vol.110, no.5, pp.257-262, 2018 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 110 Issue: 5
  • Publication Date: 2018
  • Doi Number: 10.1016/j.ygeno.2017.11.002
  • Journal Name: GENOMICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.257-262
  • Keywords: Retrotransposons, Transcription factors, Gene regulation, Mammalian genomes, Bioinformatics, TRANSPOSABLE ELEMENTS, BINDING, NETWORK, IMPACT, SHAPE
  • Dokuz Eylül University Affiliated: Yes


In recent years, retrotransposons have gained increasing attention as a source of binding motifs for transcription factors (TFs). Despite the substantial roles of these mobile genetic elements in the regulation of gene expression, a comprehensive resource enabling the investigation of retrotransposon species that are bound by TFs is still lacking. Herein, I introduce for the first time a novel database called RTFAdb, which allows exploring computationally predicted associations between retrotransposons and TFs in diverse cell lines and tissues of human and mouse. My database, using over 3.000 TF ChIP-seq binding profiles collected from human and mouse samples, makes possible searching more than 1.500 retrotransposon species in the binding sites of a total of 596 TFs. RTFAdb is freely available at http://tools.ibg.deu.edu.tr/rtfa and has the potential to offer novel insights into mammalian transcriptional networks by providing an additional layer of information regarding the regulatory roles of retrotransposons.