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Series GSE6140 Query DataSets for GSE6140
Status Public on Oct 28, 2006
Title Cross platform microarray analysis for robust identification of differentially expressed genes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, and may represent an alternative that is complementary to RT-PCR for identification of the more robust changes in gene expression profiles.
In this paper, we combined statistical and functional analysis for the cross platform validation of two oligonucleotide-based technologies, Affymetrix (AFFX) and Applied Biosystems (ABI), and for the identification of differentially expressed genes.

In this study, we analysed differentially expressed genes after treatment of an ovarian carcinoma cell line with a cell cycle inhibitor. Treated versus control RNA was analysed for expression of 16425 genes represented on both platforms.
We assessed reproducibility between replicates for each platform using CAT plots, and we found it high for both, with better scores for AFFX. We then applied integrative correlation analysis to assess reproducibility of gene expression patterns across studies, bypassing the need for normalizing expression measurements across platforms. We identified 930 genes as differentially expressed on AFFX and 908 on ABI, with ~80% common to both platforms. Despite the different absolute values, the range of intensities of the differentially expressed genes detected by each platform was similar. ABI showed a slightly higher dynamic range in FC values, which might be associated with its detection system. 62/66 genes identified as differentially expressed by Microarray were confirmed by RT-PCR.

In this study we present a cross-platform validation of two oligonucleotide-based technologies, AFFX and ABI. We found good reproducibility between replicates, and showed that both platforms can be used to select differentially expressed genes with substantial agreement. Pathway analysis of the affected functions identified themes well in agreement with those expected for a cell cycle inhibitor, suggesting that this procedure is appropriate to facilitate the identification of biologically relevant signatures associated with compound treatment. The high rate of confirmation found for both common and platform-specific genes suggests that the combination of platforms may overcome biases related to probe design and technical features, thereby accelerating the identification of trustworthy differentially expressed genes.

accepted for publication on BMC Bioinformatics
Keywords: platform comparison
 
Overall design Three biological replicates were performed for treatment and control. Biological replicates were pooled to obtain a unique sample for treatment or control, which was then divided to generate three aliquots for each condition (technical replicates) per platform.
 
Contributor(s) Bosotti R, Locatelli G, Sandra H, Scacheri E, Sartori L, Mercurio C, Calogero R, Isacchi A
Citation(s) 17430572
Submission date Oct 26, 2006
Last update date Mar 25, 2019
Contact name Roberta Bosotti
E-mail(s) roberta.bosotti@nervianoms.com
Organization name Nerviano Medical Sciences srl
Department Biotechnology
Lab Genomics
Street address viale Pasteur,10
City Nerviano
State/province MI
ZIP/Postal code 20014
Country Italy
 
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL1426 ABI Human Genome Survey Microarray Version 1
Samples (12)
GSM142447 A2780_6h_rep1
GSM142448 A2780_6h_rep2
GSM142449 A2780_6h_rep3
Relations
BioProject PRJNA97707

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Supplementary file Size Download File type/resource
GSE6140_RAW.tar 28.4 Mb (http)(custom) TAR (of CEL)

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