原创力文档reder rbioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations红色rbioconductor包代表模块化结构,网络和多级嵌套层次关联.pdfVIP
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reder rbioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations红色rbioconductor包代表模块化结构,网络和多级嵌套层次关联
Castro et al. Genome Biology 2012, 13:R29
/2012/13/4/R29
SOFTWARE Open Access
RedeR: R/Bioconductor package for representing
modular structures, nested networks and multiple
levels of hierarchical associations
*
Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer and Florian Markowetz
Abstract
Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a
large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we
present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks.
The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in
gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results
demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex
biological systems. RedeR is available from /packages/release/bioc/html/RedeR.html.
Rationale RedeR is designed to deal with three key challenges in
Biological networks contain modules of genes or pro- network analysis. Firstly, biological networks are modu-
teins that may function in the same pathway [1]. As lar and hierarchical, so network visualization needs to
genes or proteins inside a module can be co-regulated, take advantage of such structural features to avoid clut-
they are often represented by one single node in the tered and uninformative ‘hairballs’. Secondly, network
network [2]. Such modules can be i
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