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MS-kNN: protein function prediction by integrating multiple data sources

BACKGROUND: Protein function determination is a key challenge in the post-genomic era. Experimental determination of protein functions is accurate, but time-consuming and resource-intensive. A cost-effective alternative is to use the known information about sequence, structure, and functional proper...

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Autores principales: Lan, Liang, Djuric, Nemanja, Guo, Yuhong, Vucetic, Slobodan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584913/
https://www.ncbi.nlm.nih.gov/pubmed/23514608
http://dx.doi.org/10.1186/1471-2105-14-S3-S8
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author Lan, Liang
Djuric, Nemanja
Guo, Yuhong
Vucetic, Slobodan
author_facet Lan, Liang
Djuric, Nemanja
Guo, Yuhong
Vucetic, Slobodan
author_sort Lan, Liang
collection PubMed
description BACKGROUND: Protein function determination is a key challenge in the post-genomic era. Experimental determination of protein functions is accurate, but time-consuming and resource-intensive. A cost-effective alternative is to use the known information about sequence, structure, and functional properties of genes and proteins to predict functions using statistical methods. In this paper, we describe the Multi-Source k-Nearest Neighbor (MS-kNN) algorithm for function prediction, which finds k-nearest neighbors of a query protein based on different types of similarity measures and predicts its function by weighted averaging of its neighbors' functions. Specifically, we used 3 data sources to calculate the similarity scores: sequence similarity, protein-protein interactions, and gene expressions. RESULTS: We report the results in the context of 2011 Critical Assessment of Function Annotation (CAFA). Prior to CAFA submission deadline, we evaluated our algorithm on 1,302 human test proteins that were represented in all 3 data sources. Using only the sequence similarity information, MS-kNN had term-based Area Under the Curve (AUC) accuracy of Gene Ontology (GO) molecular function predictions of 0.728 when 7,412 human training proteins were used, and 0.819 when 35,622 training proteins from multiple eukaryotic and prokaryotic organisms were used. By aggregating predictions from all three sources, the AUC was further improved to 0.848. Similar result was observed on prediction of GO biological processes. Testing on 595 proteins that were annotated after the CAFA submission deadline showed that overall MS-kNN accuracy was higher than that of baseline algorithms Gotcha and BLAST, which were based solely on sequence similarity information. Since only 10 of the 595 proteins were represented by all 3 data sources, and 66 by two data sources, the difference between 3-source and one-source MS-kNN was rather small. CONCLUSIONS: Based on our results, we have several useful insights: (1) the k-nearest neighbor algorithm is an efficient and effective model for protein function prediction; (2) it is beneficial to transfer functions across a wide range of organisms; (3) it is helpful to integrate multiple sources of protein information.
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spelling pubmed-35849132013-03-11 MS-kNN: protein function prediction by integrating multiple data sources Lan, Liang Djuric, Nemanja Guo, Yuhong Vucetic, Slobodan BMC Bioinformatics Proceedings BACKGROUND: Protein function determination is a key challenge in the post-genomic era. Experimental determination of protein functions is accurate, but time-consuming and resource-intensive. A cost-effective alternative is to use the known information about sequence, structure, and functional properties of genes and proteins to predict functions using statistical methods. In this paper, we describe the Multi-Source k-Nearest Neighbor (MS-kNN) algorithm for function prediction, which finds k-nearest neighbors of a query protein based on different types of similarity measures and predicts its function by weighted averaging of its neighbors' functions. Specifically, we used 3 data sources to calculate the similarity scores: sequence similarity, protein-protein interactions, and gene expressions. RESULTS: We report the results in the context of 2011 Critical Assessment of Function Annotation (CAFA). Prior to CAFA submission deadline, we evaluated our algorithm on 1,302 human test proteins that were represented in all 3 data sources. Using only the sequence similarity information, MS-kNN had term-based Area Under the Curve (AUC) accuracy of Gene Ontology (GO) molecular function predictions of 0.728 when 7,412 human training proteins were used, and 0.819 when 35,622 training proteins from multiple eukaryotic and prokaryotic organisms were used. By aggregating predictions from all three sources, the AUC was further improved to 0.848. Similar result was observed on prediction of GO biological processes. Testing on 595 proteins that were annotated after the CAFA submission deadline showed that overall MS-kNN accuracy was higher than that of baseline algorithms Gotcha and BLAST, which were based solely on sequence similarity information. Since only 10 of the 595 proteins were represented by all 3 data sources, and 66 by two data sources, the difference between 3-source and one-source MS-kNN was rather small. CONCLUSIONS: Based on our results, we have several useful insights: (1) the k-nearest neighbor algorithm is an efficient and effective model for protein function prediction; (2) it is beneficial to transfer functions across a wide range of organisms; (3) it is helpful to integrate multiple sources of protein information. BioMed Central 2013-02-28 /pmc/articles/PMC3584913/ /pubmed/23514608 http://dx.doi.org/10.1186/1471-2105-14-S3-S8 Text en Copyright ©2013 Lan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Lan, Liang
Djuric, Nemanja
Guo, Yuhong
Vucetic, Slobodan
MS-kNN: protein function prediction by integrating multiple data sources
title MS-kNN: protein function prediction by integrating multiple data sources
title_full MS-kNN: protein function prediction by integrating multiple data sources
title_fullStr MS-kNN: protein function prediction by integrating multiple data sources
title_full_unstemmed MS-kNN: protein function prediction by integrating multiple data sources
title_short MS-kNN: protein function prediction by integrating multiple data sources
title_sort ms-knn: protein function prediction by integrating multiple data sources
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584913/
https://www.ncbi.nlm.nih.gov/pubmed/23514608
http://dx.doi.org/10.1186/1471-2105-14-S3-S8
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