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Bioinformatics (Oxford, England)
09 15, 2022;38 (18): 4430-4433.

TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments.

Federico Ansaloni, Nicolò Gualandi, Mauro Esposito, Stefano Gustincich, Remo Sanges
Author Information
  1. Federico Ansaloni: Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy. ORCID
  2. Nicolò Gualandi: Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy.
  3. Mauro Esposito: Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy.
  4. Stefano Gustincich: Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy.
  5. Remo Sanges: Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy.
PMID: 35876845 DOI: 10.1093/bioinformatics/btac526

Abstract

SUMMARY: Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts.
AVAILABILITY AND IMPLEMENTATION: The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331).
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Grants

  1. /International School for Advanced Studies
  2. /Istituto Italiano di Tecnologia
  3. /International School for Advanced Studies

MeSH Term

DNA Transposable Elements
Consensus
RNA-Seq
High-Throughput Nucleotide Sequencing
Bias

Chemicals

DNA Transposable Elements
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 6

Word Cloud

Created with Highcharts 10.0.0expressionTEquantificationfragmentstranscriptsTEstoolsdevelopedembeddedcanonicalTEspeXreadsavailableSUMMARY:TransposableelementsplaykeyrolescrucialbiologicalpathwaysThereforeseveralenablingrecentlyHowevermanyexistinglackcapabilitydistinguishtranscriptionautonomouslyexpressedcoding/non-codingnon-TEConsequentlyapparentchangegivenmaysimplyreflectvariationcontainingTE-derivedsequencesovercomeissuepipelineconsensuslevelusesIlluminaRNA-seqshortquantifyavoidingcountingderivinginactiveAVAILABILITYANDIMPLEMENTATION:toolimplementedpython3distributedGNUGeneralPublicLicenseGPLGithubhttps://githubcom/fansalon/TEspeXZenodoURL:https://doiorg/105281/zenodo6800331SUPPLEMENTARYINFORMATION:SupplementarydataBioinformaticsonlineTEspeX:consensus-specifictransposableelementpreventingbiasesexonized

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