title: Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis.
abstract: Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.
authors.affiliation: Department of Electrical Engineering , Faculty of Engineering, Katholieke Universiteit Leuven, B-3001 Heverlee, Belgium.
authors.forename: Joke
authors.initials: J
authors.lastname: Allemeersch
authors.forename: Steffen
authors.initials: S
authors.lastname: Durinck
authors.forename: Rudy
authors.initials: R
authors.lastname: Vanderhaeghen
authors.forename: Philippe
authors.initials: P
authors.lastname: Alard
authors.forename: Ruth
authors.initials: R
authors.lastname: Maes
authors.forename: Kurt
authors.initials: K
authors.lastname: Seeuws
authors.forename: Tom
authors.initials: T
authors.lastname: Bogaert
authors.forename: Kathleen
authors.initials: K
authors.lastname: Coddens
authors.forename: Kirsten
authors.initials: K
authors.lastname: Deschouwer
authors.forename: Paul
authors.initials: P
authors.lastname: Van Hummelen
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.forename: Yves
authors.initials: Y
authors.lastname: Moreau
authors.forename: Jeroen
authors.initials: J
authors.lastname: Kwekkeboom
authors.forename: André H M
authors.initials: AH
authors.lastname: Wijfjes
authors.forename: Sean
authors.initials: S
authors.lastname: May
authors.forename: Jim
authors.initials: J
authors.lastname: Beynon
authors.forename: Pierre
authors.initials: P
authors.lastname: Hilson
authors.forename: Martin T R
authors.initials: MT
authors.lastname: Kuiper
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D005188:False Negative Reactions; D005189:False Positive Reactions; D015870:Gene Expression; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger; D018749:RNA, Plant / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant