T3E: TRANSPOSABLE ELEMENT ENRICHMENT ESTIMATOR

Michelle Almeida da Paz*, Leila Taher

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference paperpeer-review

Abstract

Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.
Original languageEnglish
Title of host publicationProceedings Annual Meeting of the Austrian Society for Biomedical Engineering 2021
Subtitle of host publicationÖGBMT 2021
PublisherVerlag der Technischen Universität Graz
Pages95-98
Number of pages4
DOIs
Publication statusPublished - 2021
EventAnnual Meeting of the Austrian Society of the Biomedical Engineering 2021: ÖGBMT 2021 - Graz University of Technology, Graz, Austria
Duration: 30 Sep 20211 Oct 2021
https://oegbmt2021.tugraz.at/

Conference

ConferenceAnnual Meeting of the Austrian Society of the Biomedical Engineering 2021
Abbreviated titleÖGBMT 2021
Country/TerritoryAustria
CityGraz
Period30/09/211/10/21
Internet address

Keywords

  • Transposable element
  • enrichment
  • ChIP-seq
  • histone modifications

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