Year: 2021
Type: article
Abstract: Network medicine has proven useful for dissecting genetic organization of complex human diseases. We have previously published HumanNet, an integrated network of human genes for disease studies. Since the release of the last version of HumanNet, many large-scale protein-protein interaction datasets have accumulated in public depositories. Additionally, the numbers of research papers and functional annotations for gene-phenotype associations have increased significantly. Therefore, updating HumanNet is a timely task for further improvement of network-based research into diseases. Here, we present HumanNet v3 (https://www.inetbio.org/humannet/, covering 99.8% of human protein coding genes) constructed by means of the expanded data with improved network inference algorithms. HumanNet v3 supports a three-tier model: HumanNet-PI (a protein-protein physical interaction network), HumanNet-FN (a functional gene network), and HumanNet-XC (a functional network extended by co-citation). Users can select a suitable tier of HumanNet for their study purpose. We showed that on disease gene predictions, HumanNet v3 outperforms both the previous HumanNet version and other integrated human gene networks. Furthermore, we demonstrated that HumanNet provides a feasible approach for selecting host genes likely to be associated with COVID-19.
Source: Nucleic Acids Research
DOI: 10.1093/nar/gkab1048
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,800
Awards: G1258467559, G4816134225, G5487401516, G5631022149, G6043510538, G6578395119, Proteomics and model organism humanization to decode human genetics, Deciphering the hierarchical modularity of the mammalian cell through network integration and complex genetic perturbation strategies, Cancer Center Support Grant
OpenAlex ID: W3211778832