title: RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.
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 http://bioconductor.org/packages/release/bioc/html/RedeR.html.
authors.affiliation: Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Mauro A A
authors.initials: MA
authors.lastname: Castro
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.forename: Michael N C
authors.initials: MN
authors.lastname: Fletcher
authors.forename: Kerstin B
authors.initials: KB
authors.lastname: Meyer
authors.forename: Florian
authors.initials: F
authors.lastname: Markowetz
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015203:Reproducibility of Results; D012984:Software; D024363:Transcription Initiation Site