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NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks
Large amounts of various biological networks exist for representing different types of interaction data, such as genetic, metabolic, gene regulatory, and protein-protein relationships. Recent approaches on biological network study are based on different mathematical concepts. It is necessary to cons...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322572/ https://www.ncbi.nlm.nih.gov/pubmed/28280740 http://dx.doi.org/10.1155/2017/7457131 |
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author | Cao, Yang Xu, Wenjian Niu, Chao Bo, Xiaochen Li, Fei |
author_facet | Cao, Yang Xu, Wenjian Niu, Chao Bo, Xiaochen Li, Fei |
author_sort | Cao, Yang |
collection | PubMed |
description | Large amounts of various biological networks exist for representing different types of interaction data, such as genetic, metabolic, gene regulatory, and protein-protein relationships. Recent approaches on biological network study are based on different mathematical concepts. It is necessary to construct a uniform framework to judge the functionality of biological networks. We recently introduced a knowledge-based computational framework that reliably characterized biological networks in system level. The method worked by making systematic comparisons to a set of well-studied “basic networks,” measuring both the functional and topological similarities. A biological network could be characterized as a spectrum-like vector consisting of similarities to basic networks. Here, to facilitate the application, development, and adoption of this framework, we present an R package called NFP. This package extends our previous pipeline, offering a powerful set of functions for Network Fingerprint analysis. The software shows great potential in biological network study. The open source NFP R package is freely available under the GNU General Public License v2.0 at CRAN along with the vignette. |
format | Online Article Text |
id | pubmed-5322572 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-53225722017-03-09 NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks Cao, Yang Xu, Wenjian Niu, Chao Bo, Xiaochen Li, Fei Biomed Res Int Research Article Large amounts of various biological networks exist for representing different types of interaction data, such as genetic, metabolic, gene regulatory, and protein-protein relationships. Recent approaches on biological network study are based on different mathematical concepts. It is necessary to construct a uniform framework to judge the functionality of biological networks. We recently introduced a knowledge-based computational framework that reliably characterized biological networks in system level. The method worked by making systematic comparisons to a set of well-studied “basic networks,” measuring both the functional and topological similarities. A biological network could be characterized as a spectrum-like vector consisting of similarities to basic networks. Here, to facilitate the application, development, and adoption of this framework, we present an R package called NFP. This package extends our previous pipeline, offering a powerful set of functions for Network Fingerprint analysis. The software shows great potential in biological network study. The open source NFP R package is freely available under the GNU General Public License v2.0 at CRAN along with the vignette. Hindawi Publishing Corporation 2017 2017-02-09 /pmc/articles/PMC5322572/ /pubmed/28280740 http://dx.doi.org/10.1155/2017/7457131 Text en Copyright © 2017 Yang Cao et al. https://creativecommons.org/licenses/by/4.0/ 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 Cao, Yang Xu, Wenjian Niu, Chao Bo, Xiaochen Li, Fei NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title | NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title_full | NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title_fullStr | NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title_full_unstemmed | NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title_short | NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks |
title_sort | nfp: an r package for characterizing and comparing of annotated biological networks |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322572/ https://www.ncbi.nlm.nih.gov/pubmed/28280740 http://dx.doi.org/10.1155/2017/7457131 |
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