title: A comparison of oligonucleotide and cDNA-based microarray systems.
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.
authors.affiliation: First Department of Medicine, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany.
authors.forename: Nancy
authors.initials: N
authors.lastname: Mah
authors.forename: Anders
authors.initials: A
authors.lastname: Thelin
authors.forename: Tim
authors.initials: T
authors.lastname: Lu
authors.forename: Susanna
authors.initials: S
authors.lastname: Nikolaus
authors.forename: Tanja
authors.initials: T
authors.lastname: Kühbacher
authors.forename: Yesim
authors.initials: Y
authors.lastname: Gurbuz
authors.forename: Holger
authors.initials: H
authors.lastname: Eickhoff
authors.forename: Günther
authors.initials: G
authors.lastname: Klöppel
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Björn
authors.initials: B
authors.lastname: Mellgård
authors.forename: Christine M
authors.initials: CM
authors.lastname: Costello
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
mesh_terms: D000368:Aged; D020087:Alu Elements / Q000235:genetics; D001706:Biopsy; D003106:Colon / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D018076:DNA, Complementary; D009841:Oligonucleotides; D012333:RNA, Messenger