Can subtle changes in gene expression be consistently detected with different microarray platforms?

Pedotti, Paola; 't Hoen, Peter A. C.; Vreugdenhil, Erno; Schenk, Geert J.; Vossen, Rolf H. A. M.; Ariyurek, Yavuz; de Hollander, Mattias; Kuiper, Rowan; van Ommen, Gertjan J. B.; den Dunnen, Johan T.; Boer, Judith M.; de Menezes, Renée X.
January 2008
BMC Genomics;2008, Vol. 9, Special section p1
Academic Journal
Background: The comparability of gene expression data generated with different microarray platforms is still a matter of concern. Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle. Results: Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina, LGTC home-spotted arrays. Using a fixed false discovery rate of 10% we detected surprising differences between the number of differentially expressed genes per platform. Four genes were selected by ABI, 130 by Affymetrix, 3,051 by Agilent, 54 by Illumina, and 13 by LGTC. Two genes were found significantly differentially expressed by all platforms and the four genes identified by the ABI platform were found by at least three other platforms. Quantitative RT-PCR analysis confirmed 20 out of 28 of the genes detected by two or more platforms and 8 out of 15 of the genes detected by Agilent only. We observed improved correlations between platforms when ranking the genes based on the significance level than with a fixed statistical cut-off. We demonstrate significant overlap in the affected gene sets identified by the different platforms, although biological processes were represented by only partially overlapping sets of genes. Aberrances in GABA-ergic signalling in the transgenic mice were consistently found by all platforms. Conclusion: The different microarray platforms give partially complementary views on biological processes affected. Our data indicate that when analyzing samples with only subtle differences in gene expression the use of two different platforms might be more attractive than increasing the number of replicates. Commercial two-color platforms seem to have higher power for finding differentially expressed genes between groups with small differences in expression.


Related Articles

  • Artefacts and Reliability of DNA Microarray Expression Profiling Data. Drobyshev, Alexei L.; de Angelis, Martin Hrabe; Beckers, Johannes // Current Genomics;Oct2003, Vol. 4 Issue 7, p615 

    Microarray expression profiling is a complex experimental methodology comprising sequential steps: fluorescent or radioactive labelling of extracted RNA, hybridisation to the array, washing, scanning, and image processing of the array and data analysis. Each of these steps is a possible source...

  • Construction of a reference gene association network from multiple profiling data: application to data analysis. Ucar, Duygu; Neuhaus, Isaac; Ross-MacDonald, Petra; Tilford, Charles; Parthasarathy, Srinivasan; Siemers, Nathan; Rui-Ru Ji // Bioinformatics;Oct2007, Vol. 23 Issue 20, p2716 

    Motivation: Gene expression profiling is an important tool for gaining insight into biology. Novel strategies are required to analyze the growing archives of microarray data and extract useful information from them. One area of interest is in the construction of gene association networks from...

  • Expression Profiling of Endocrine-Disrupting Compounds Using a Customized Cyprinus carpio cDNA Microarray. Moens, Lotte N.; Van der Ven, Karlijn; Remortel, Piet Van; Del-Favero, Jurgen; De Coen, Wim M. // Toxicological Sciences;Oct2006, Vol. 93 Issue 2, p298 

    Exposure to a variety of anthropogenic compounds has been shown to interfere with normal development, physiology, and reproduction in a wide range of organisms, both in laboratory studies and wildlife. We have developed a Cyprinus carpio cDNA microarray consisting of endocrine-related genes. In...

  • Genome-wide Gene Expression Analysis for Induced Ischemic Tolerance and Delayed Neuronal Death Following Transient Global Ischemia in Rats. Nobutaka Kawahara // Journal of Cerebral Blood Flow & Metabolism;Feb2004, Vol. 24 Issue 2, p212 

    SUMMARY: Genome-wide gene expression analysis of the hippocampal CA1 region was conducted in a rat global ischemia model for delayed neuronal death and induced ischemic tolerance using an oligonucleotide-based DNA microarray containing 8,799 probes. The results showed that expression levels of...

  • Effects of delayed motherhood on hippocampal gene expression in offspring rats. Xing, Ying; Duan, Ping; Li, Bo; Li, Caifang; Han, Xuefei; Xu, Yan; Yan, Wenhai // Molecular & Cellular Biochemistry;Jul2015, Vol. 405 Issue 1/2, p89 

    While many studies have examined the pregnancy and health-related outcomes of delayed motherhood for women, less is known concerning the potential consequences for their children. This study aims to investigate the effect of delayed motherhood on the hippocampus at the whole genome level....

  • Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. Zollanvari, Amin; Cunningham, Mary Jane; Braga-Neto, Ulisses; Dougherty, Edward R. // BMC Bioinformatics;2009 Supplement 11, Vol. 10, Special section p1 

    Background: Nanomaterials are being manufactured on a commercial scale for use in medical, diagnostic, energy, component and communications industries. However, concerns over the safety of engineered nanomaterials have surfaced. Humans can be exposed to nanomaterials in different ways such as...

  • Defining a transcriptional fingerprint of murine splenic B-cell development. Debnath, I; Roundy, K. M.; Dunn, D. M.; Weiss, R. B.; Weis, J. J.; Weis, J. H. // Genes & Immunity;Dec2008, Vol. 9 Issue 8, p706 

    B-cell development occurs in a stepwise fashion that can be followed by the expression of B cell-specific surface markers. In this study, we wished to identify proteins that could contribute to the changes in expression of such markers. By using RNA from freshly isolated B220+ cells, we hoped to...

  • cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model. Kluger, Harriet M.; Kluger, Yuval; Gilmore-Hebert, Maureen; DiVito, Kyle; Chang, Joseph T.; Rodov, Sofya; Mironenko, Olga; Kacinski, Barry M.; Perkins, Archibald S.; Sapi, Eva // Laboratory Investigation (00236837);Mar2004, Vol. 84 Issue 3, p320 

    The fms oncogene encodes the macrophage colony-stimulating factor receptor (CSF1R), a transmembrane tyrosine kinase receptor, which is abnormally expressed in breast cancer. Transfection of wild-type CSF1R into HC11 mammary epithelial cells (HC11-CSF1R) renders the transfectants capable of in...

  • Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. Jonnalagadda, Sudhakar; Srinivasan, Rajagopalan // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, measured between different biological conditions. These differentially...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics