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TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability.

Hao Jiang1, Zhicheng Xu1, Tong Li1

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The Transcriptome Turnover Database (TTDB) centralizes mRNA decay rate data from numerous studies. This resource aids researchers in understanding gene expression regulation across five species.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Messenger mRNA turnover is crucial for regulating gene expression levels.
  • High-throughput sequencing generates extensive transcriptome-wide mRNA decay data.
  • Existing mRNA stability data is fragmented across many publications, hindering analysis.

Purpose of the Study:

  • To create a centralized, comprehensive resource for genome-wide mRNA stability data.
  • To facilitate the harmonization and comparison of mRNA decay rates.
  • To provide a user-friendly platform for accessing and analyzing mRNA turnover information.

Main Methods:

  • Integrated 198 high-throughput datasets from 57 publications.
  • Standardized mRNA half-lives and decay rates computationally.
  • Collected data for five species: human, mouse, zebrafish, fruit fly, and yeast.

Main Results:

  • Developed the Transcriptome Turnover Database (TTDB).
  • TTDB includes data for an average of 12,544 genes per dataset.
  • Provided precomputed annotations for transcripts, including GC content and regulatory elements.

Conclusions:

  • TTDB offers a valuable, centralized resource for mRNA stability data.
  • The database simplifies the study of gene expression regulation.
  • TTDB is publicly accessible via a web interface for broad research use.