<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Microarrays and tag-based transcriptional profiling technologies represent diverse
but complementary data types. We are currently conducting a comparison of high-density
<italic>in situ</italic> synthesized microarrays and massively-parallel signature sequencing
(MPSS) data in the model plant, <italic>Arabidopsis thaliana</italic>. The MPSS data (available at
http://mpss.udel.edu/at) and the microarray data have been compiled using the same
RNA source material. In this review, we outline the experimental strategy that we
are using, and present preliminary data and interpretations from the transcriptional
profiles of <italic>Arabidopsis</italic> leaves and roots. The preliminary data indicate that the log
ratio differences of transcripts between leaves and roots measured by microarray data
are in better agreement with the MPSS data than the absolute intensities measured
for individual microarrays hybridized to only one of the cRNA populations. The
correlation was substantially improved by focusing on a subset of genes excluding
those with very low expression levels; this selection may have removed noisy data.
Future reports will incorporate more than 10 tissues that have been sampled by
MPSS.</p>
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Comp Funct Genomics. 2004 Apr; 5(3):245-252