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5'SAGE: 5'-end Serial Analysis of Gene Expression database
Yasuhiro Kasai1, Shin-ichi Hashimoto, Tomoyuki Yamada
1Department of Computational Biology, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashinoha, Kashiwa City, Chiba 277-8562, Japan.
Nucleic Acids Research
|December 21, 2004
Summary
A new method, 5' end Serial Analysis of Gene Expression (SAGE), identifies human transcription start sites and mRNA frequencies. The 5'SAGE database aids in analyzing gene promoter regions and start site variations across tissues.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Accurate identification of transcription start sites (TSS) is crucial for understanding gene regulation.
- Existing methods may not comprehensively capture the full spectrum of TSS and mRNA frequencies.
Purpose of the Study:
- To develop and present a novel method for identifying human transcription start sites and mRNA frequencies.
- To establish the 5'SAGE database for accessible analysis of this data.
Main Methods:
- Utilized 5' end Serial Analysis of Gene Expression (SAGE) to collect extensive transcription start site information.
- Developed the 5'SAGE database to store and display observed frequencies of 5' end SAGE tags and identified TSS.
Main Results:
- Successfully identified numerous transcription start sites, including previously unknown ones in promoter, intronic, and intergenic regions.
- The 5'SAGE database provides observed frequencies for individual 5' end SAGE tags.
Conclusions:
- The 5' end SAGE method and the 5'SAGE database offer a powerful resource for comprehensive analysis of transcription start sites.
- This resource will facilitate studies on promoter regions and transcription start site variation in different human tissues.