What is iHypoxia
The iHypoxia is a hypoxia associated protein database, which collated 692 literatures for 5 mammals hypoxia research. In total, 158,615 quantification events on 41,482 hypoxia-regulated proteins under 390 conditions/states were collected and integrated in the database. Various browse and search options are provided in the database, and the detailed information is organized and visualized for queries.
Hypoxia is a condition or state in which insufficient levels of oxygen are supplied to cells or tissues. The research of hypoxia mainly studies physiological and pathological changes under hypoxic conditions and reveal its role in diseases, tumors, biological processes and so on.
How to use Hypoxia
In the home page of iHypoxia, users can start a quick search with the keyword(s) of interest or simply click an example that we provided above the input field and search button to perform an example search.
In the part of data browse for low-throughput experiment, the diagram shows the number of hypoxia associated proteins with evidence from low-throughput experiment (LTE) in different organisms. Users can click one bar to view all the LTE-associated proteins of a certain organism, and the results are shown in the table on the right. Then, users can click the 'More' button in the table to see the detailed information of interested protein.
In the part of data browse for high-throughput experiment, the diagram shows the number of conditions for evidence from high-throughput experiment (HTE) of hypoxia association in different organisms. Users can click one bar to view all the HTE-associated conditions of a certain organism, then the results are shown in the table on the right. By clicking the 'View' button in the table, users can see all the significantly different proteins of the chosen condition and the results are shown in the table at the bottom, while users can click the 'More' button in this table to see the detailed information of interested protein.
In the Search page, users can enter a keyword of Ensembl ID, UniProt ID, Gene name or Protein name to search the related information, and all matched results will be shown in the table below. Also, we have provided some examples for each search type, and Users can just click one example and the “Search” button to perform an example search.
The result page shows the results that users are interested and users can get more detailed results by click the 'More' button.
Hypoxia reference resources
Ensembl is a genome browser for vertebrate genomes that supports researches in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotates genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.http://www.ensembl.org/
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.https://www.uniprot.org/
HypoxiaDB is a first ever manually-curated non-redundant catalogue of human hypoxia-regulated proteins with a goal of collecting proteins whose expression patterns are altered in hypoxic conditions. It is a highly curated database providing information on expression pattern changes under different levels and duration of hypoxia. HypoxiaDB currently contains more than 72,000 entries taken on 3,500 differentially regulated proteins extracted from 73 peer-reviewed publications and ~1,500 supporting publications.http://www.hypoxiadb.com/
HRGFish is a database of hypoxia responsive genes in fishes, and covers 818 gene sequences and 35 gene types from 38 fishes.http://mail.nbfgr.res.in/HRGFish
Gene Ontology (GO)
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.http://geneontology.org/