iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals

Mammals have evolved mechanisms to sense hypoxia and induce hypoxic responses. Recently, high-throughput techniques have greatly promoted global studies of protein expression changes during hypoxia and the identification of candidate genes associated with hypoxia-adaptive evolution, which have contributed to the understanding of the complex regulatory net-works of hypoxia. In this study, we developed an integrated resource for the expression dynamics of proteins in response to hypoxia (iHypoxia), and this database contains 2589 expression events of 1944 proteins identified by low-throughput experiments (LTEs) and 422,553 quantitative expres-sion events of 33,559 proteins identified by high-throughput experiments from five mammals that exhibit a response to hypoxia. Various experimental details, such as the hypoxic experimental con-ditions, expression patterns, and sample types, were carefully collected and integrated. Further-more, 8788 candidate genes from diverse species inhabiting low-oxygen environments were also integrated. In addition, we conducted an orthologous search and computationally identified 394,141 proteins that may respond to hypoxia among 48 animals. An enrichment analysis of human proteins identified from LTEs shows that these proteins are enriched in certain drug targets and cancer genes. Annotation of known posttranslational modification (PTM) sites in the proteins iden-tified by LTEs reveals that these proteins undergo extensive PTMs, particularly phosphorylation, ubiquitination, and acetylation. iHypoxia provides a convenient and user-friendly method for users to obtain hypoxia-related information of interest. We anticipate that iHypoxia, which is freely accessible at https://ihypoxia.omicsbio.info, will advance the understanding of hypoxia and serve as a valuable data resource.

Automated summary

In this study, we developed an integrated resource (iHypoxia) for the expression dynamics of proteins in response to hypoxia. The database contains expression data of proteins from multiple mammals, candidate genes associated with hypoxia, and information about posttranslational modifications. iHypoxia provides a convenient way for users to access hypoxia-related information.