Gill Ryan, Datta Somnath, Datta Susmita
Department of Mathematics, University of Louisville, Louisville, KY 40292 USA.
Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40292 USA.
Bioinformation. 2014 Apr 23;10(4):233-4. doi: 10.6026/97320630010233. eCollection 2014.
Differential network analysis provides a framework for examining if there is sufficient statistical evidence to conclude that the structure of a network differs under two experimental conditions or if the structures of two networks are different. The R package dna provides tools and procedures for differential network analysis of genomic data. The focus of this package is on gene-gene networks, but the methods are easily adaptable for more general biological processes. This package includes preprocessing tools for simultaneously preparing a pair of networks for analysis, procedures for computing connectivity scores between pairs of genes based on many available statistical techniques, and tools for handling modules of genes based on these scores. Also, procedures are provided for performing permutation tests based on these scores to determine if the connectivity of a gene differs between the two networks, to determine if the connectivity of a particular set of important genes differs between the two networks, and to determine if the overall module structure differs between the two networks. Several built-in options are available for the types of scores and distances used in the testing procedures, and additionally, the procedures provide flexible methods that allow the user to define custom scores and distances.
dna is freely available at The Comprehensive R Archive Network, http://CRAN.R-project.org/package=dna.
差异网络分析提供了一个框架，用于检验是否有足够的统计证据来得出结论，即一个网络的结构在两种实验条件下是否不同，或者两个网络的结构是否不同。R包dna提供了用于基因组数据差异网络分析的工具和程序。该包的重点是基因-基因网络，但这些方法很容易适用于更一般的生物过程。这个包包括用于同时准备一对网络进行分析的预处理工具、基于许多可用统计技术计算基因对之间连通性得分的程序，以及基于这些得分处理基因模块的工具。此外，还提供了基于这些得分进行置换检验的程序，以确定一个基因的连通性在两个网络之间是否不同，确定一组特定重要基因的连通性在两个网络之间是否不同，以及确定两个网络之间的整体模块结构是否不同。测试程序中使用的得分和距离类型有几种内置选项，此外，这些程序还提供了灵活的方法，允许用户定义自定义得分和距离。
dna可在综合R存档网络（http://CRAN.R-project.org/package=dna）上免费获取。
