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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents

ID: 229815.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
A comparison of oligonucleotide and cDNA-based microarray systems
Authors:Mah, Nancy; Thelin, Anders; Lu, Tim; Nikolaus, Susanna; Kuehbacher, Tanja; Gurbuz, Yesim; Eickhoff, Holger; Kloeppel, Guenther; Lehrach, Hans; Mellgård, Bjoern; Costello, Christine M.; Schreiber, Stefan
Date of Publication (YYYY-MM-DD):2004-02-13
Title of Journal:Physiological Genomics
Journal Abbrev.:Physiol Genomics
Issue / Number:16
Start Page:361
End Page:370
Copyright:© 2004 by the American Physiological Society
Review Status:not specified
Audience:Experts Only
Abstract / Description:Large-scale public data mining will become more common as public release of microarray data sets becomes a corequisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely, an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in "present" or "absent" calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors, or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms.
Free Keywords:noncommercial clone-based microarray system; commercial oligonucleotide-based microarray system; expression screening platform; cross-platform screening
Comment of the Author/Creator:First published November 25, 2003; doi:10.1152/physiolgenomics.00080.2003
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:First Department of Medicine, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany;
AstraZeneca R&D Moelndal, S-43183 Moelndal, Sweden;
Department of Pathology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany.
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