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Performing Custom MicroRNA Microarray Experiments
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rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays.

Frieder Hadlich1, Henry Reyer1, Michael Oster1

  • 1Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, D-18196 Dummerstorf, Germany.

Genomics, Proteomics & Bioinformatics
|February 13, 2021
PubMed
Summary

The rePROBE R package updates gene expression microarray probe annotations using current genomic and transcriptomic data. This enhances accuracy for expression quantitative trait locus (eQTL) studies across multiple species.

Keywords:
Genomic databaseMappingMicroarrayProbe assignmentProbe-set annotation

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Commercial and custom microarrays are essential for analyzing gene expression patterns.
  • Accurate probe assignment and annotation are critical for reliable microarray data analysis.
  • Existing microarray platforms require frequent updates with the latest genomic and transcriptomic information.

Purpose of the Study:

  • To develop a comprehensive workflow for updating probe and probe set annotations on gene expression microarrays.
  • To create an R package, rePROBE, for automating probe re-assignment and annotation using current biological data.
  • To improve the accuracy and utility of microarrays for expression analysis and downstream applications like eQTL studies.

Main Methods:

  • Implementation of a workflow in the R programming language to process genomic and transcriptomic data.
  • Utilizing public databases (RefSeq, Ensembl) and custom data for probe annotation.
  • Application of the rePROBE package to commercial microarray platforms for chicken, pig, cattle, human, and mouse.

Main Results:

  • The rePROBE workflow successfully re-annotated probes and probe sets across multiple species, including livestock and model organisms.
  • Updated annotations identified a significant number of unique genes and their positions, enhancing the biological relevance of microarray data.
  • The workflow also incorporated single nucleotide polymorphism (SNP) data, facilitating expression quantitative trait locus (eQTL) studies.

Conclusions:

  • The rePROBE R package provides a robust and up-to-date solution for microarray probe annotation, crucial for accurate gene expression analysis.
  • This tool enhances the value of existing microarray platforms by integrating current genomic and transcriptomic information.
  • The enhanced annotation and SNP data availability support advanced genetic analyses, including the identification of genes influencing quantitative and functional traits.