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Related Experiment Videos

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Hideya Kawaji1, Takeya Kasukawa, Shiro Fukuda

  • 1NTT Software Corporation, Teisan Kannai Building 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan.

Nucleic Acids Research
|December 31, 2005
PubMed
Summary

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The Cap-analysis gene expression (CAGE) databases provide millions of human and mouse CAGE tags for identifying and characterizing novel promoters. These resources are crucial for understanding gene expression profiles across various tissues and conditions.

Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • The Cap-analysis gene expression (CAGE) method sequences transcript 5' ends to identify transcription start sites.
  • Large-scale CAGE data provides insights into gene expression patterns and promoter activity.

Purpose of the Study:

  • To present the CAGE Basic and Analysis Databases, which store and organize CAGE data.
  • To facilitate the identification and characterization of novel promoters and transcriptional units.

Main Methods:

  • Sequencing of millions of human and mouse CAGE tags from diverse tissues and conditions.
  • Development of CAGE Basic and Analysis Databases to store and analyze CAGE data.
  • Utilizing CAGE tag starting sites and clusters to define promoters and transcriptional units.

Related Experiment Videos

Main Results:

  • The databases contain millions of high-quality CAGE tags from over 20 human and mouse tissues.
  • Promoter-related information, including transcript counts, CpG islands, and conserved regions, is stored.
  • Expression profiles at base pair and promoter levels are provided.

Conclusions:

  • The CAGE databases offer a comprehensive resource for promoter discovery and characterization.
  • These databases support the Functional Annotation Of Mouse 3 (FANTOM3) project and are freely accessible.
  • The integrated framework enables detailed analysis of transcriptional units and promoter associations.