A comparison of global gene expression measurement technologies in Arabidopsis thaliana

Sean J. Coughlan, Vikas Agrawal, Blake Meyers

Research output: Contribution to journalReview articlepeer-review

16 Scopus citations


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 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 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 wiih 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.

Original languageEnglish
Pages (from-to)245-252
Number of pages8
JournalComparative and Functional Genomics
Issue number3
StatePublished - Apr 2004


  • Cross-platform comparisons
  • Gene expression
  • MPSS
  • Microarrays


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