Measuring phenotype-phenotype similarity through the interactome
Abstract Background Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may l...
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| Format: | Article |
| Language: | English |
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BMC
2018-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2102-9 |
| _version_ | 1828769849078185984 |
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| author | Jiajie Peng Weiwei Hui Xuequn Shang |
| author_facet | Jiajie Peng Weiwei Hui Xuequn Shang |
| author_sort | Jiajie Peng |
| collection | DOAJ |
| description | Abstract Background Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype similarity. Results We proposed a network-based method PhenoNet to calculate the similarity between phenotypes. We localized phenotypes in the network and calculated the similarity between phenotype-associated modules by modeling both the inter- and intra-similarity. Conclusions PhenoNet was evaluated on two independent evaluation datasets: gene ontology and gene expression data. The result shows that PhenoNet performs better than the state-of-art methods on all evaluation tests. |
| first_indexed | 2024-12-11T13:56:18Z |
| format | Article |
| id | doaj.art-6f1f7140c44a4ca881abe3871f4794f8 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T13:56:18Z |
| publishDate | 2018-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-6f1f7140c44a4ca881abe3871f4794f82022-12-22T01:04:03ZengBMCBMC Bioinformatics1471-21052018-04-0119S5657710.1186/s12859-018-2102-9Measuring phenotype-phenotype similarity through the interactomeJiajie Peng0Weiwei Hui1Xuequn Shang2School of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversitySchool of Computer Science, Northwestern Polytechnical UniversityAbstract Background Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype similarity. Results We proposed a network-based method PhenoNet to calculate the similarity between phenotypes. We localized phenotypes in the network and calculated the similarity between phenotype-associated modules by modeling both the inter- and intra-similarity. Conclusions PhenoNet was evaluated on two independent evaluation datasets: gene ontology and gene expression data. The result shows that PhenoNet performs better than the state-of-art methods on all evaluation tests.http://link.springer.com/article/10.1186/s12859-018-2102-9Phenotype relationshipsInteractomeHuman phenotype ontology |
| spellingShingle | Jiajie Peng Weiwei Hui Xuequn Shang Measuring phenotype-phenotype similarity through the interactome BMC Bioinformatics Phenotype relationships Interactome Human phenotype ontology |
| title | Measuring phenotype-phenotype similarity through the interactome |
| title_full | Measuring phenotype-phenotype similarity through the interactome |
| title_fullStr | Measuring phenotype-phenotype similarity through the interactome |
| title_full_unstemmed | Measuring phenotype-phenotype similarity through the interactome |
| title_short | Measuring phenotype-phenotype similarity through the interactome |
| title_sort | measuring phenotype phenotype similarity through the interactome |
| topic | Phenotype relationships Interactome Human phenotype ontology |
| url | http://link.springer.com/article/10.1186/s12859-018-2102-9 |
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