title: NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks.
abstract: 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.
authors.affiliation: Department of Biotechnology, Beijing Institute of Radical Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China; Tianjin Institute of Health & Environmental Medicine, 1 Dali Road, Heping District, Tianjin 300050, China.
authors.forename: Yang
authors.identifier: 0000-0001-7787-8506
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Department of Biotechnology, Beijing Institute of Radical Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China.
authors.forename: Wenjian
authors.initials: W
authors.lastname: Xu
authors.affiliation: Tianjin Institute of Health & Environmental Medicine, 1 Dali Road, Heping District, Tianjin 300050, China.
authors.forename: Chao
authors.identifier: 0000-0002-0416-0613
authors.initials: C
authors.lastname: Niu
authors.affiliation: Department of Biotechnology, Beijing Institute of Radical Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China.
authors.forename: Xiaochen
authors.identifier: 0000-0003-1911-7922
authors.initials: X
authors.lastname: Bo
authors.affiliation: Department of Biotechnology, Beijing Institute of Radical Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China.
authors.forename: Fei
authors.identifier: 0000-0003-4895-7330
authors.initials: F
authors.lastname: Li
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D015398:Signal Transduction / Q000235:genetics; D012984:Software