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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
PIGOK: Linking protein identity to gene ontology and function
Richard J Jacob1, Rainer Cramer
1Department of Biochemistry, University College London, Gower Street, London WC1E 6BT, United Kingdom.
Journal of Proteome Research
|December 2, 2006
Summary
We developed PIGOK, a computer database for retrieving protein physicochemical properties, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes data. This tool aids in identifying biological functions and pathways, as demonstrated by analyzing oxidative stress-responsive proteins in Schizosaccharomyces pombe.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- Understanding protein function is crucial for biological research.
- Accessing integrated protein data, including physicochemical properties and functional annotations, can be challenging.
- Existing databases may not offer rapid retrieval for specific analyses.
Purpose of the Study:
- To introduce PIGOK, a novel computer database for efficient retrieval of protein information.
- To facilitate the analysis of protein properties, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
- To demonstrate the utility of PIGOK in identifying biological functions and pathways of differentially expressed proteins.
Main Methods:
- Development of a computer database for storing and querying protein data.
- Integration of physicochemical properties, GO terms, and KEGG pathways.
- Application of the PIGOK database to analyze proteins from Schizosaccharomyces pombe.
- Analysis focused on proteins exhibiting differential expression under oxidative stress conditions.
Main Results:
- The PIGOK database enables rapid retrieval of comprehensive protein information.
- Analysis of Schizosaccharomyces pombe proteins identified key biological functions and pathways related to oxidative stress.
- The study successfully demonstrated the application of PIGOK for functional genomics research.
Conclusions:
- PIGOK provides a valuable resource for researchers studying protein function and pathways.
- The database streamlines the process of integrating diverse protein data for analysis.
- PIGOK is a powerful tool for investigating cellular responses to stress, exemplified by its use in yeast research.
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