Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://www.translatomedb.net/
Full name: Translatome Database
Description: TranslatomeDB provides collection and integrated analysis of published and user-generated translatome sequencing data.
Year founded: 2018
Last update: 2018
Version: 1.0
Accessibility:
Manual:
Accessible
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Country/Region: China
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Jinan University
Address: Chi-Biotech Co. Ltd., Shenzhen 518000, China
City: Guangzhou
Province/State: Guangdong
Country/Region: China
Contact name (PI/Team): Gong Zhang
Contact email (PI/Helpdesk): zhanggong@jnu.edu.cn

Publications

29106630
TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data. [PMID: 29106630]
Wanting Liu, Lunping Xiang, Tingkai Zheng, Jingjie Jin, Gong Zhang,

Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power.

Nucleic Acids Res.. 2017:() | 13 Citations (from Europe PMC, 2021-05-01)

Ranking

All databases:
1979/5030 (60.676%)
Raw bio-data:
162/486 (66.872%)
Gene genome and annotation:
598/1343 (55.547%)
Metadata:
172/495 (65.455%)
1979
Total Rank
13
Citations
3.25
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Created on: 2021-03-24
Curated by:
lin liu [2021-03-24]
Feng Changrui [2021-03-24]