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- Publisher Website: 10.1007/s11424-010-0207-y
- Scopus: eid_2-s2.0-84866672238
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Article: On Network-based Kernel Methods for Protein-Protein Interactions with Applications in Protein Functions Prediction
Title | On Network-based Kernel Methods for Protein-Protein Interactions with Applications in Protein Functions Prediction |
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Authors | |
Keywords | Diffusion kernel Kernel method Laplacian kernel Local linear embedding (LLE) kernel Protein function prediction Support vector machine |
Issue Date | 2010 |
Publisher | Springer Verlag. The Journal's web site is located at http://link.springer.com/journal/11424 |
Citation | Journal of Systems Science and Complexity, 2010, v. 23 n. 5, p. 917-930 How to Cite? |
Abstract | Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding (LLE) kernel method, diffusion kernel and laplacian kernel to uncover the relationship between proteins functions and protein-protein interactions (PPI). The author first construct kernels based on PPI networks, then apply support vector machine (SVM) techniques to classify proteins into different functional groups. The 5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chi-square methods. Finally, the authors conduct predictions of functions of some unknown genes and verify the preciseness of our prediction in part by the information of other data source. |
Persistent Identifier | http://hdl.handle.net/10722/129255 |
ISSN | 2023 Impact Factor: 2.6 2023 SCImago Journal Rankings: 0.705 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Li, L | en_US |
dc.contributor.author | Ching, W | en_US |
dc.contributor.author | Chan, Y | en_US |
dc.contributor.author | Mamitsuka, H | en_US |
dc.date.accessioned | 2010-12-23T08:34:14Z | - |
dc.date.available | 2010-12-23T08:34:14Z | - |
dc.date.issued | 2010 | en_US |
dc.identifier.citation | Journal of Systems Science and Complexity, 2010, v. 23 n. 5, p. 917-930 | en_US |
dc.identifier.issn | 1009-6124 | - |
dc.identifier.uri | http://hdl.handle.net/10722/129255 | - |
dc.description.abstract | Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding (LLE) kernel method, diffusion kernel and laplacian kernel to uncover the relationship between proteins functions and protein-protein interactions (PPI). The author first construct kernels based on PPI networks, then apply support vector machine (SVM) techniques to classify proteins into different functional groups. The 5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chi-square methods. Finally, the authors conduct predictions of functions of some unknown genes and verify the preciseness of our prediction in part by the information of other data source. | - |
dc.language | eng | en_US |
dc.publisher | Springer Verlag. The Journal's web site is located at http://link.springer.com/journal/11424 | en_US |
dc.relation.ispartof | Journal of Systems Science and Complexity | en_US |
dc.rights | The original publication is available at www.springerlink.com | en_US |
dc.subject | Diffusion kernel | - |
dc.subject | Kernel method | - |
dc.subject | Laplacian kernel | - |
dc.subject | Local linear embedding (LLE) kernel | - |
dc.subject | Protein function prediction | - |
dc.subject | Support vector machine | - |
dc.subject.mesh | Diffusion kernel | - |
dc.subject.mesh | Kernel method | - |
dc.subject.mesh | Laplacians | - |
dc.subject.mesh | Local Linear Embedding | - |
dc.subject.mesh | Protein function prediction | - |
dc.title | On Network-based Kernel Methods for Protein-Protein Interactions with Applications in Protein Functions Prediction | en_US |
dc.type | Article | en_US |
dc.identifier.email | Ching, W: wching@hkucc.hku.hk | en_US |
dc.identifier.email | Chan, Y: wtymchan@hku.hk | en_US |
dc.identifier.authority | Ching, WK=rp00679 | en_US |
dc.identifier.doi | 10.1007/s11424-010-0207-y | - |
dc.identifier.scopus | eid_2-s2.0-84866672238 | - |
dc.identifier.hkuros | 183321 | en_US |
dc.identifier.volume | 23 | en_US |
dc.identifier.issue | 5 | - |
dc.identifier.spage | 917 | en_US |
dc.identifier.epage | 930 | en_US |
dc.identifier.isi | WOS:000284074000005 | - |
dc.publisher.place | China | - |
dc.identifier.issnl | 1009-6124 | - |