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Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis
M Ishii1, S Hashimoto, S Tsutsumi
1Genome Science Division, Research Center for Advanced Science and Technology, Tokyo, Japan.
Genomics
|August 31, 2000
Summary
This study compared two gene expression analysis methods: oligonucleotide arrays and Serial Analysis of Gene Expression (SAGE). Results show good correlation, suggesting oligonucleotide arrays are reliable for expression profiling.
Area of Science:
- Molecular Biology
- Genomics
Background:
- High-throughput transcript expression analysis is crucial in molecular biology.
- Oligonucleotide arrays and Serial Analysis of Gene Expression (SAGE) are common methods.
Purpose of the Study:
- To compare the quantitative accuracy of oligonucleotide arrays and SAGE.
- To evaluate GeneChip technology for expression profiling.
Main Methods:
- Both methods were applied to identical RNA specimens from human monocytes and GM-CSF-induced macrophages.
- SAGE yielded ~28,000 unique tags; GeneChip analyzed ~6000 transcripts.
Main Results:
- Oligonucleotide arrays and SAGE showed good correlation in absolute and comparative expression analyses.
- Correlation improved for genes with higher expression levels and greater changes.
Conclusions:
- GeneChip technology demonstrates reasonable reliability for quantitative expression profiling.
- Oligonucleotide arrays are suitable for building gene expression databases.