Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells.

Seraya Maouche,Ivo Gut,Robert Olaso,Gilles Montalescot,Jean-Phillipe Collet,Tiphaine Godefroy,Odette Poirier,François Cambien

doi:10.1186/1471-2164-9-302

Abstract

BackgroundIn this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. Five RNA samples for each type of cell were hybridized to the two platforms in parallel. In addition, a reference list of differentially expressed genes (DEG) was generated from a larger number of hybridizations (mRNA from 86 individuals) using the RNG/MRC two-color platform.ResultsOur results show an important overlap of the Illumina and Affymetrix DEG lists. In addition, more than 70% of the genes in these lists were also present in the reference list. Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant for the biology of monocytes and macrophages. Our results support the conclusion of the MicroArray Quality Control (MAQC) project that the criteria used to constitute the DEG lists strongly influence the degree of concordance among platforms. However the importance of prioritizing genes by magnitude of effect (fold change) rather than statistical significance (p-value) to enhance cross-platform reproducibility recommended by the MAQC authors was not supported by our data.ConclusionFunctional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference list.

Highlights

In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes
The present study was designed to evaluate the ability of 2 commonly utilized microarray technologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes
For the data generated on the Réseau National des Génopoles/Medical Research Council (RNG/MRC) platform we investigated several background correction and within/between array normalization methods implemented in the Linear Model for Microarray Data (Limma) and marray packages

Summary

Introduction

In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. The primary goal of the MAQC project was to evaluate the technical variability of DNA microarray results obtained with a number of different microarray technologies. The MAQC results showed relatively low technical variability in the intra-site and inter-site measurements, and high inter-platforms concordance for the thousands of genes identified as differentially expressed between 2 reference RNA samples explored under 4 titration conditions [10,11]. The present study was designed to evaluate the ability of 2 commonly utilized microarray technologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. M-CSF induced activation of monocytes for 6 days leads to differential regulation of a large number of genes, and offers the possibility to compare the microarray platforms across a wide range of differential gene expressions

Methods

Results

Discussion

Conclusion