Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Cao, Yang, Xu, Wenjian, Niu, Chao, Bo, Xiaochen, Li, Fei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2017
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
_version_ 1782509872418390016
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
work_keys_str_mv AT caoyang nfpanrpackageforcharacterizingandcomparingofannotatedbiologicalnetworks
AT xuwenjian nfpanrpackageforcharacterizingandcomparingofannotatedbiologicalnetworks
AT niuchao nfpanrpackageforcharacterizingandcomparingofannotatedbiologicalnetworks
AT boxiaochen nfpanrpackageforcharacterizingandcomparingofannotatedbiologicalnetworks
AT lifei nfpanrpackageforcharacterizingandcomparingofannotatedbiologicalnetworks