Toward elucidating the global gene expression patternsof developing Arabidopsis: Parallel analysis of 8 300 genesby a high-density oligonucleotide probe array

Abstract

Arabidopsis thaliana has been widely used as a model system, in various aspects of biological studies, such as genomics, genetics, cellular, developmental and molecular biology. In order to reveal the molecular events and regulatory networks controlling Arabidopsis development and responses to genetic and environmental changes, we designed and used a high-density oligonucleotide probe array (GeneChip) to profile global gene expression patterns. The Arabidopsis oligonucleotide probe array consists of probes from 8 300 unique Arabidopsis genes, which covers approximately one-third of the genome. Global transcription profiles of A. thaliana in various developmental stages, and their responses to different environments were generated using this microarray, and archived. Here, we analyze data sets derived from nineteen independent experiments. Constitutively and differentially expressed genes in seedlings, roots, leaves, inflorescences, flowers and siliques at different developmental stages were identified. Functions of these genes based on homologs were determined and categorized. Our results provide insight into the coordinated transcriptional regulation of the genes during plant growth and development.