ArticleNucleic acids research2009
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 88 citations in OpenAlex.
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- Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection.Frontiers in genetics · 2021Article
- Oral lichen planus interactome reveals CXCR4 and CXCL12 as candidate therapeutic targets.Scientific reports · 2020Article
- Computational Methods for Identifying Similar Diseases.Molecular therapy. Nucleic acids · 2019Review
- HMNPPID-human malignant neoplasm protein-protein interaction database.Human genomics · 2019Article
- Simulation of the Dynamics of Primary Immunodeficiencies in B Cells.Frontiers in immunology · 2018Article
- Measuring disease similarity and predicting disease-related ncRNAs by a novel method.BMC medical genomics · 2017Article
- DisSetSim: an online system for calculating similarity between disease sets.Journal of biomedical semantics · 2017Article
- Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry.Scientific reports · 2017Article
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- Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins.Scientific reports · 2016Article
- SGFSC: speeding the gene functional similarity calculation based on hash tables.BMC bioinformatics · 2016Article
- Fusing literature and full network data improves disease similarity computation.BMC bioinformatics · 2016Article
- CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types.Oncogenesis · 2015Article
- Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer.Nature communications · 2015Article
- Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers.Journal of cellular and molecular medicine · 2015Review
- Predicting Abdominal Aortic Aneurysm Target Genes by Level-2 Protein-Protein Interaction.PloS one · 2015Article
- Application of centrality measures in the identification of critical genes in diabetes mellitus.Bioinformation · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Disease gene identification is still a challenge despite modern high-throughput methods. Many diseases are very rare or lethal and thus cannot be investigated with traditional methods. Several in silico methods have been developed but they have some limitations. We introduce a new method that combines information about protein-interaction network properties and Gene Ontology terms. Genes with high-calculated network scores and statistically significant gene ontology terms based on known diseases are prioritized as candidate genes. The method was applied to identify novel primary immunodeficiency-related genes, 26 of which were found. The investigation uses the protein-interaction network for all essential immunome human genes available in the Immunome Knowledge Base and an analysis of their enriched gene ontology annotations. The identified disease gene candidates are mainly involved in cellular signaling including receptors, protein kinases and adaptor and binding proteins as well as enzymes. The method can be generalized for any disease group with sufficient information.
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