Abstract
There has been intense interest in the cellular response to hypoxia, and a large number of differentially expressed proteins have been identified through various high-throughput experiments. These valuable data are scattered, and there have been no systematic attempts to document the various proteins regulated by hypoxia. Compilation, curation and annotation of these data are important in deciphering their role in hypoxia and hypoxia-related disorders. Therefore, we have compiled HypoxiaDB, a database of hypoxia-regulated proteins. It is a comprehensive, manually-curated, non-redundant catalog of proteins whose expressions are shown experimentally to be altered at different levels and durations of hypoxia. The database currently contains 72 000 manually curated entries taken on 3500 proteins extracted from 73 peer-reviewed publications selected from PubMed. HypoxiaDB is distinctive from other generalized databases: (i) it compiles tissue-specific protein expression changes under different levels and duration of hypoxia. Also, it provides manually curated literature references to support the inclusion of the protein in the database and establish its association with hypoxia. (ii) For each protein, HypoxiaDB integrates data on gene ontology, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, protein–protein interactions, protein family (Pfam), OMIM (Online Mendelian Inheritance in Man), PDB (Protein Data Bank) structures and homology to other sequenced genomes. (iii) It also provides pre-compiled information on hypoxia-proteins, which otherwise requires tedious computational analysis. This includes information like chromosomal location, identifiers like Entrez, HGNC, Unigene, Uniprot, Ensembl, Vega, GI numbers and Genbank accession numbers associated with the protein. These are further cross-linked to respective public databases augmenting HypoxiaDB to the external repositories. (iv) In addition, HypoxiaDB provides an online sequence-similarity search tool for users to compare their protein sequences with HypoxiaDB protein database. We hope that HypoxiaDB will enrich our knowledge about hypoxia-related biology and eventually will lead to the development of novel hypothesis and advancements in diagnostic and therapeutic activities. HypoxiaDB is freely accessible for academic and non-profit users via http://www.hypoxiadb.com.Database URL: http://www.hypoxiadb.com
Highlights
Hypoxia is a pathophysiological condition and refers to an abnormally low partial pressure of oxygen in atmosphere, low content of oxygen dissolved in per liter of blood or less percentage saturation of hemoglobin with oxygen, either found singly or in combination [1, 2]
Each protein symbol is linked to the corresponding protein page, which contains detailed information about the protein and its expression changes in hypoxia
The user can browse through the complete alphabetical list of proteins. (ii) Browse by category: This option allows the user to browse through the list of proteins according to the categories listed below: (a) List of upregulated and downregulated proteins: Using this option, the user can retrieve a list of proteins that are up/downregulated during hypoxia
Summary
Hypoxia is a pathophysiological condition and refers to an abnormally low partial pressure of oxygen in atmosphere, low content of oxygen dissolved in per liter of blood or less percentage saturation of hemoglobin with oxygen, either found singly or in combination [1, 2]. Different levels and duration of hypoxia cause varying adverse effects from time to time. It may occur in diseased conditions (like cancers, malignancies, etc) or may be induced by environmental factors. The blood supply is restricted in tumor tissue region, which leads to tumor hypoxia [3]. Almost 140 million people in the world (representing 2% of the world’s human population) reside in high altitudes (8000 ft above sea level) and are continuously ß The Author(s) 2013.
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