Comparison of transcript proﬁling on Arabidopsis microarray
Jeffrey D. Pylatuik and Pierre R. Fobert*
Plant Biotechnology Institute National Research Council Canada, 110 Gymnasium Place, S7N 0W9,
Saskatoon, Saskatchewan, Canada (*author for correspondence; e-mail Pierre.Fobert@nrc-cnrc.gc.ca)
Received 1 March 2005; accepted in revised form 26 April 2005
Key words: GeneChip, Genomic Amplicon, long oligonucleotide, Northern blot, systemic acquired
To date there have been few systematic studies comparing the results of transcript proﬁling from diﬀerent
microarray platform technologies. We evaluated in detail two diﬀerent Arabidopsis thaliana microarray
platforms: our own Genomic Amplicon arrays and the Qiagen long oligonucleotide arrays designed by
Operon; furthermore, we cross-validated these arrays against the Aﬀymetrix AG and ATH1 GeneChips.
Data were obtained from all three platforms in each of two separate experiments; (1) at 2 h and (2) 8 h
following a salicylic acid treatment applied to both wild-type and npr1–3 mutant plants. A total of 20
hybridizations were performed, analyzing the expression of 26 814 unique locusIDs. We demonstrate that
intensity rank is a key variable that aﬀects both inter-platform and cross-platform reproducibility.
Although general agreement between platform technologies is low, data derived from high signal intensities
(90th percentile) can correlate as well between diﬀering platforms as replicates within the same platform
(r = 0.4–0.7). We also show that the identiﬁcation of diﬀerentially expressed genes by signiﬁcance analysis
of microarrays is inﬂuenced by signal intensity and that overlap between signiﬁcant gene lists from diﬀerent
platform technologies was as high as 67% when low intensity values were removed. Validation of 41 genes
by Northern blot hybridization showed that all platform technologies performed well, qualitatively con-
ﬁrming 83–100% of diﬀerential gene expression. Our results suggest that the potential for the broad
integration of microarray data from diﬀerent platforms and laboratories is promising.
The number of published studies using microarray
technology is increasing rapidly (Kothapalli et al.,
2002; Li et al., 2002; Marshall, 2004), resulting in a
huge resource of data. Tapping the full potential of
this resource requires the ability to merge existing
data generated by multiple microarray platforms.
Some platform technologies involve fabrication by
post-synthesis spotting of nucleic acid targets onto
a solid substrate, usually glass microscope slides.
Spotted platforms are typically deﬁned by the
nucleotide source from which the target was made.
Common spotted platforms include cDNA micro-
arrays (Schena et al., 1995), where targets are
derived from cDNA libraries and long oligonu-
cleotide microarrays derived from synthetic nucle-
otides 50–80 bp in length (Kane et al., 2000,
Qiagen Inc.; BD Biosciences). A less common
alternative for spotted array targets (particularly
in eukaryotic systems) is the use of Genomic
Amplicons (Kim et al., 2003, Hilson et al., 2004).
Another platform technology, marketed by
Affymetrix, uses in situ synthesis of short target
Plant Molecular Biology (2005) 58:609–624 Ó Springer 2005