Cargando…

Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations

The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was develo...

Descripción completa

Detalles Bibliográficos
Autores principales: Suratanee, Apichat, Plaimas, Kitiporn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513527/
https://www.ncbi.nlm.nih.gov/pubmed/28757797
http://dx.doi.org/10.1177/1177932217720405
_version_ 1783250680251678720
author Suratanee, Apichat
Plaimas, Kitiporn
author_facet Suratanee, Apichat
Plaimas, Kitiporn
author_sort Suratanee, Apichat
collection PubMed
description The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (RkNN) search. The RkNN search was used to identify an impact of a protein on other proteins. Then, associations between proteins and diseases were inferred statistically. The method using the RkNN search yielded a much higher precision than a random selection, standard nearest neighbor search, or when applying the method to a random protein-protein interaction network. All protein-disease pair candidates were verified by a literature search. Supporting evidence for 596 pairs was identified. In addition, cluster analysis of these candidates revealed 10 promising groups of diseases to be further investigated experimentally. This method can be used to identify novel associations to better understand complex relationships between proteins and diseases.
format Online
Article
Text
id pubmed-5513527
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher SAGE Publications
record_format MEDLINE/PubMed
spelling pubmed-55135272017-07-28 Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations Suratanee, Apichat Plaimas, Kitiporn Bioinform Biol Insights Original Research The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (RkNN) search. The RkNN search was used to identify an impact of a protein on other proteins. Then, associations between proteins and diseases were inferred statistically. The method using the RkNN search yielded a much higher precision than a random selection, standard nearest neighbor search, or when applying the method to a random protein-protein interaction network. All protein-disease pair candidates were verified by a literature search. Supporting evidence for 596 pairs was identified. In addition, cluster analysis of these candidates revealed 10 promising groups of diseases to be further investigated experimentally. This method can be used to identify novel associations to better understand complex relationships between proteins and diseases. SAGE Publications 2017-07-13 /pmc/articles/PMC5513527/ /pubmed/28757797 http://dx.doi.org/10.1177/1177932217720405 Text en © The Author(s) 2017 http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page(https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Original Research
Suratanee, Apichat
Plaimas, Kitiporn
Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title_full Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title_fullStr Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title_full_unstemmed Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title_short Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations
title_sort reverse nearest neighbor search on a protein-protein interaction network to infer protein-disease associations
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513527/
https://www.ncbi.nlm.nih.gov/pubmed/28757797
http://dx.doi.org/10.1177/1177932217720405
work_keys_str_mv AT surataneeapichat reversenearestneighborsearchonaproteinproteininteractionnetworktoinferproteindiseaseassociations
AT plaimaskitiporn reversenearestneighborsearchonaproteinproteininteractionnetworktoinferproteindiseaseassociations