Inference of gene-phenotype associations via protein-protein interaction and orthology.
One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple speci...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3806783?pdf=render |
| _version_ | 1828878371755393024 |
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| author | Panwen Wang Wing-Fu Lai Mulin Jun Li Feng Xu Hari Krishna Yalamanchili Robin Lovell-Badge Junwen Wang |
| author_facet | Panwen Wang Wing-Fu Lai Mulin Jun Li Feng Xu Hari Krishna Yalamanchili Robin Lovell-Badge Junwen Wang |
| author_sort | Panwen Wang |
| collection | DOAJ |
| description | One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth. |
| first_indexed | 2024-12-13T09:03:50Z |
| format | Article |
| id | doaj.art-049ceb798341444088742aae81ccaa40 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T09:03:50Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-049ceb798341444088742aae81ccaa402022-12-21T23:53:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01810e7747810.1371/journal.pone.0077478Inference of gene-phenotype associations via protein-protein interaction and orthology.Panwen WangWing-Fu LaiMulin Jun LiFeng XuHari Krishna YalamanchiliRobin Lovell-BadgeJunwen WangOne of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.http://europepmc.org/articles/PMC3806783?pdf=render |
| spellingShingle | Panwen Wang Wing-Fu Lai Mulin Jun Li Feng Xu Hari Krishna Yalamanchili Robin Lovell-Badge Junwen Wang Inference of gene-phenotype associations via protein-protein interaction and orthology. PLoS ONE |
| title | Inference of gene-phenotype associations via protein-protein interaction and orthology. |
| title_full | Inference of gene-phenotype associations via protein-protein interaction and orthology. |
| title_fullStr | Inference of gene-phenotype associations via protein-protein interaction and orthology. |
| title_full_unstemmed | Inference of gene-phenotype associations via protein-protein interaction and orthology. |
| title_short | Inference of gene-phenotype associations via protein-protein interaction and orthology. |
| title_sort | inference of gene phenotype associations via protein protein interaction and orthology |
| url | http://europepmc.org/articles/PMC3806783?pdf=render |
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