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

Genomics. 2018 Sep;110(5):257-262. doi: 10.1016/j.ygeno.2017.11.002. Epub 2017 Nov 17.

Abstract

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.

Keywords: Bioinformatics; Gene regulation; Mammalian genomes; Retrotransposons; Transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic*
  • Gene Regulatory Networks*
  • Genome, Human
  • Humans
  • Mice
  • Protein Binding
  • Retroelements*
  • Software*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*

Substances

  • Retroelements
  • Transcription Factors