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Comparative and Functional Genomics
Volume 5 (2004), Issue 3, Pages 245-252
Conference review

A Comparison of Global Gene Expression Measurement Technologies in Arabidopsis thaliana

1Agilent Technologies Inc., Little Falls Site, 2850 Centerville Road, Wilmington, DE 19808- 1644, USA
2Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA

Received 10 February 2004; Revised 12 February 2004; Accepted 12 February 2004

Copyright © 2004 Hindawi Publishing Corporation. 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.


Microarrays and tag-based transcriptional profiling technologies represent diverse but complementary data types. We are currently conducting a comparison of high-density in situ synthesized microarrays and massively-parallel signature sequencing (MPSS) data in the model plant, Arabidopsis thaliana. The MPSS data (available 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 Arabidopsis 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.