PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants


Karakulah G., Suner Karakülah A.

GENOMICS, vol.109, pp.336-340, 2017 (Journal Indexed in SCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 109
  • Publication Date: 2017
  • Doi Number: 10.1016/j.ygeno.2017.05.008
  • Title of Journal : GENOMICS
  • Page Numbers: pp.336-340
  • Keywords: Transposable elements, Gene regulation, Plant genomes, Database, Bioinformatics, MESSENGER-RNA TRANSCRIPTION, EPIGENETIC REGULATION, RETROTRANSPOSONS, EVOLUTION, STRESS, CONSEQUENCES, EXPRESSION, GENOMES

Abstract

Transposable elements (TEs) are mobile DNA sequences that play roles in gene regulation, and have a potential to influence the expression of nearby genes by functioning as cis-regulatory sequences. However, bioinformatics tools facilitating analysis of the associations between TEs and nearby genes in plants are still lacking. We therefore reanalyzed the comprehensive annotation data of gene models and TEs of 11 plant species available in Ensembl Plants database, and built an up-to-date, unique tool called PlanTEnrichment, enabling enrichment analysis of TEs located within the upstream regions of a given gene list. PlanTEnrichment takes, for example, a group of differentially expressed genes under a particular biological condition as input and returns the list of TEs associated with those genes, along with their calculated enrichment scores and statistical significances. PlanTEnrichment is freely available at http://tools.ibg.deu.edu.tr/plantenrichment/ and is likely to substantially enhance our understanding of the role of TEs in diverse biological processes. (C) 2017 Elsevier Inc. All rights reserved.