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  A comparison of oligonucleotide and cDNA-based microarray systems

Mah, N., Thelin, A., Lu, T., Nikolaus, S., Kuehbacher, T., Gurbuz, Y., et al. (2004). A comparison of oligonucleotide and cDNA-based microarray systems. Physiological Genomics, 13(16), 361-370. doi:1094-8341/04.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-88CD-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-88CE-1
Genre: Journal Article
Alternative Title : Physiol Genomics

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 Creators:
Mah, Nancy, Author
Thelin, Anders, Author
Lu, Tim, Author
Nikolaus, Susanna, Author
Kuehbacher, Tanja, Author
Gurbuz, Yesim, Author
Eickhoff, Holger1, Author
Kloeppel, Guenther, Author
Lehrach, Hans2, Author              
Mellgård, Bjoern, Author
Costello, Christine M., Author
Schreiber, Stefan, Author
Affiliations:
1Max Planck Society, ou_persistent13              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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Free keywords: noncommercial clone-based microarray system; commercial oligonucleotide-based microarray system; expression screening platform; cross-platform screening
 Abstract: 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.

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Language(s): eng - English
 Dates: 2004-02-13
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 229815
DOI: 1094-8341/04
 Degree: -

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Title: Physiological Genomics
  Alternative Title : Physiol Genomics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 13 (16) Sequence Number: - Start / End Page: 361 - 370 Identifier: ISSN: 1094-8341