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PaGenBase: a pattern gene database for the global and dynamic understanding of gene function.
Jian-Bo Pan1, Shi-Chang Hu, Dan Shi
1Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, PR China.
Plos One
|December 7, 2013
Summary
PaGenBase is a new database that collects tissue- and time-specific pattern genes. This resource aids in understanding gene functions during development and disease, facilitating novel drug discovery.
Area of Science:
- Genomics
- Bioinformatics
- Systems Biology
Background:
- Pattern genes exhibit modular expression across physiological conditions.
- Identifying pattern genes is crucial for understanding gene function in biological processes like development and pathogenesis.
Purpose of the Study:
- To introduce PaGenBase, a novel repository for tissue- and time-specific pattern genes.
- To provide a freely accessible database for pattern gene retrieval and analysis.
Main Methods:
- Collected and curated 906,599 pattern genes from literature and gene expression profiles.
- Utilized data from 1,145,277 gene expression profiles across 1,062 samples in 11 model organisms.
- Developed four statistical parameters for quantitative evaluation and three search methods for data retrieval.
Main Results:
- PaGenBase 1.0 contains a comprehensive collection of pattern genes.
- The database offers efficient data retrieval through quick search, advanced search, and browse functionalities.
- Quantitative evaluation parameters and diverse data sources enhance the reliability of the collected pattern genes.
Conclusions:
- PaGenBase serves as a valuable resource for global and dynamic gene function understanding.
- Facilitates high-level research in development, pathogenesis, and drug discovery.
- Promotes a deeper insight into gene expression patterns and their biological significance.
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