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Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks
A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict prot...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333188/ https://www.ncbi.nlm.nih.gov/pubmed/25722972 http://dx.doi.org/10.1155/2015/259157 |
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author | Liu, Peng Yang, Lei Shi, Daming Tang, Xianglong |
author_facet | Liu, Peng Yang, Lei Shi, Daming Tang, Xianglong |
author_sort | Liu, Peng |
collection | PubMed |
description | A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology. |
format | Online Article Text |
id | pubmed-4333188 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-43331882015-02-26 Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks Liu, Peng Yang, Lei Shi, Daming Tang, Xianglong Biomed Res Int Research Article A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology. Hindawi Publishing Corporation 2015 2015-02-03 /pmc/articles/PMC4333188/ /pubmed/25722972 http://dx.doi.org/10.1155/2015/259157 Text en Copyright © 2015 Peng Liu et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Liu, Peng Yang, Lei Shi, Daming Tang, Xianglong Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title | Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title_full | Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title_fullStr | Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title_full_unstemmed | Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title_short | Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks |
title_sort | prediction of protein-protein interactions related to protein complexes based on protein interaction networks |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333188/ https://www.ncbi.nlm.nih.gov/pubmed/25722972 http://dx.doi.org/10.1155/2015/259157 |
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