ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays an...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2004-09, Vol.39 (5), p.697-714
Main Authors: Alba, R, Fei, Z, Payton, P, Liu, Y, Moore, S.L, Debbie, P, Cohn, J, D'Ascenzo, M, Gordon, J.S, Rose, J.K.C
Format: Article
Language:English
Subjects:
Agricultural sciences
Agronomy
Biotechnology
Capsicum annuum
complementary DNA
digital expression analysis
DNA, Complementary - genetics
Expressed Sequence Tags
expression profiling
Fluorescent Dyes
fruiting
Gene Expression Profiling
gene expression regulation
genomics
Life Sciences
literature reviews
Lycopersicon esculentum
microarray technology
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
plant development
plant physiology
plant proteins
ripening
Solanum lycopersicum var. lycopersicum
tomatoes
transcription (genetics)
transcriptome
Vegetal Biology
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Summary:Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.
ISSN:0960-7412
1365-313X
DOI:10.1111/j.1365-313x.2004.02178.x