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Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array
John Fernandes1, Volker Brendel, Xiaowu Gai
1Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
Plant Physiology
|March 14, 2002
Summary
Maize gene expression profiles reveal significant overlap between endosperm and ear tissues, despite initial low estimates. Microarray analysis highlights the importance of transcript sampling depth for accurate gene expression comparisons in plants.
Area of Science:
- Plant Genomics
- Maize Gene Expression
Background:
- Expressed sequence tags (ESTs) are crucial for understanding gene expression in plants.
- Maize (Zea mays) gene expression varies across organs and developmental stages.
Purpose of the Study:
- To quantify gene expression overlap between maize endosperm and immature ear tissues.
- To assess the accuracy of EST-based gene discovery and microarray hybridization for gene expression profiling.
Main Methods:
- Assembly of 73,000 maize ESTs to identify tentative unique genes (TUGs).
- Fabrication of custom microarray slides using endosperm and immature ear ESTs.
- Hybridization of microarrays with cDNA targets from endosperm and immature ear poly(A(+)) RNA.
Main Results:
- Initial EST assembly identified ~22,000 TUGs with low overlap (4-20%) between libraries.
- Microarray analysis revealed substantial gene expression overlap: 94% of ear TUGs detected in endosperm, and 57% of endosperm TUGs in ear.
- Abundant ESTs were often library-specific, suggesting incomplete transcript sampling.
Conclusions:
- EST sampling depth significantly impacts the estimation of shared gene expression profiles.
- Microarray hybridization can reveal greater gene expression overlap than initially suggested by EST assembly.
- Gene family member expression in distinct organs and potential overestimation of overlap in microarray experiments warrant further investigation.