The regulation of messenger mRNA turnover is a critical cellular process that dictates gene expression levels. High-throughput sequencing technologies have enabled the measurement of mRNA decay rates on a transcriptome-wide scale. However, this vast amount of data is dispersed across numerous publications, and it is cumbersome to harmonize and compare. To address this, we have developed the Transcriptome Turnover Database (TTDB), a centralized and comprehensive resource for genome-wide mRNA stability data. TTDB integrates 198 high-throughput datasets from 57 publications, with an average 12 544 genes per dataset, across five species: human, mouse, zebrafish, fruit fly, and yeast. The database not only provides experimentally determined and computationally standardized mRNA half-lives and decay rates, but also offers precomputed annotations for each transcript, including GC content, minimum free energy of mRNA secondary structure, and counts of regulatory elements like upstream AUGs and AU-rich elements. The user-friendly web interface allows users to intuitively browse, search, visualize, and download data by study, sample, or gene. TTDB is publicly accessible at https://sysbio.gzzoc.com/ttdb/index.html.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.
| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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