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What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
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Impact of gene expression data pre-processing on expression quantitative trait locus mapping.

Aurelie Labbe1,2, Marie-Paule Roth3, Pierre-Hugues Carmichael1

  • 1Département de Mathématiques et de Statistique, Université Laval, Québec, G1K 7P4, Canada.

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|May 10, 2008
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Summary
This summary is machine-generated.

Different data pre-processing methods significantly impact expression quantitative trait locus (eQTL) mapping results. Agreement between methods was higher for heritable traits and cis-acting loci.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Genomics

Background:

  • Microarray data pre-processing is crucial for downstream analyses.
  • Expression quantitative trait locus (eQ; QTL) mapping aims to link genetic variation to gene expression levels.
  • Standardized pre-processing methods are needed for reproducible eQTL studies.

Purpose of the Study:

  • To evaluate the impact of three pre-processing methods on Affymetrix microarray data for eQTL mapping.
  • To compare linkage outcomes, including the number and location of signals, and cis/trans-regulation.
  • To assess how trait selection criteria (expression level, variance, heritability) influence method agreement.

Main Methods:

  • Utilized 14 CEPH Utah families (GAW Problem 1 data).
  • Applied three distinct pre-processing methods to Affymetrix microarray data.
  • Selected expression traits based on expression level, variance, and heritability.
  • Performed whole-genome scans using multipoint variance component LOD scores for each pre-processed trait set.

Main Results:

  • Found limited agreement between linkage results across different pre-processing methods; most signals were method-specific.
  • Observed higher agreement rates for traits selected based on heritability.
  • Noted minimal impact of pre-processing on the proportion of cis- versus trans-regulating loci detected.
  • Reported better agreement for cis-regulating loci compared to trans-regulating loci, despite their smaller numbers.

Conclusions:

  • Pre-processing choices introduce significant variability in eQTL mapping results.
  • Trait heritability is a key factor influencing the concordance of eQTL findings across methods.
  • While cis-eQTLs show better agreement, the overall discordance highlights the need for careful method selection and validation in eQTL studies.