Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray

Heenam Kim, Erik C. Snesrud, Brian Haas, Foo Cheung, Christopher D. Town, John Quackenbush

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)


The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3′ ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.

Original languageEnglish
Pages (from-to)327-340
Number of pages14
JournalGenome Research
Issue number3
Publication statusPublished - 2003 Mar 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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