Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells
Open Access
- 25 June 2008
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 9 (1), 302
- https://doi.org/10.1186/1471-2164-9-302
Abstract
Background 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. 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. Results Our 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. Conclusion Functional 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.This publication has 38 references indexed in Scilit:
- Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) dataBMC Bioinformatics, 2007
- QA/QC issues to aid regulatory acceptance of microarray gene expression dataEnvironmental and Molecular Mutagenesis, 2007
- Three methods for optimization of cross-laboratory and cross-platform microarray expression dataNucleic Acids Research, 2007
- A rapid method for microarray cross platform comparisons using gene expression signaturesMolecular and Cellular Probes, 2007
- Using RNA sample titrations to assess microarray platform performance and normalization techniquesNature Biotechnology, 2006
- The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsNature Biotechnology, 2006
- Evaluation of DNA microarray results with quantitative gene expression platformsNature Biotechnology, 2006
- An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomesNucleic Acids Research, 2006
- Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesProceedings of the National Academy of Sciences of the United States of America, 2005
- A Direct Approach to False Discovery RatesJournal of the Royal Statistical Society Series B: Statistical Methodology, 2002