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HypoxiaDB: a database of hypoxia-regulated proteins
Pankaj Khurana1, Ragumani Sugadev, Jaspreet Jain
1Bioinformatics Group, Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization, Lucknow Road, Timarpur, New Delhi-110054, India.
Database : the Journal of Biological Databases and Curation
|November 2, 2013
Summary
HypoxiaDB is a new manually-curated database cataloging proteins affected by hypoxia. This resource integrates diverse data, aiding research into hypoxia-related disorders and advancing diagnostics and therapeutics.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Cellular response to hypoxia is of significant interest.
- Numerous hypoxia-regulated proteins have been identified but data is fragmented.
- Systematic compilation and annotation are crucial for understanding hypoxia's role in disease.
Purpose of the Study:
- To create HypoxiaDB, a comprehensive, manually-curated database of hypoxia-regulated proteins.
- To consolidate scattered data on proteins affected by varying hypoxia levels and durations.
- To facilitate research into hypoxia-related disorders.
Main Methods:
- Compiled and manually curated data from 73 peer-reviewed publications in PubMed.
- Included 3500 proteins with 72,000 curated entries.
- Integrated gene ontology, pathway, interaction, structural, and homology data.
- Cross-linked entries with public databases and provided pre-compiled identifiers.
- Developed an online sequence-similarity search tool.
Main Results:
- Established HypoxiaDB, a non-redundant catalog of hypoxia-regulated proteins.
- Database contains tissue-specific expression changes under different hypoxia conditions.
- Integrated comprehensive annotations including pathways, interactions, and genetic information.
- Provided direct links to external databases and a sequence search tool.
Conclusions:
- HypoxiaDB enriches understanding of hypoxia-related biology.
- The database supports the development of novel hypotheses.
- Facilitates advancements in diagnostic and therapeutic strategies for hypoxia-related conditions.
- Freely accessible for academic and non-profit users.
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