Analysis of biological networks

The concept of networks is coming from the graph theories. There are multiple packages in R and Bioconductor for reconstructing, analyzing, and simulating different networks, including the ones relevant for biological research. Networks are composed from nodes and their links. There are several network concepts in biology that one can encounter during the analysis of experimental data. Gene regulatory networks (GRNs) represent the regulatory effect of transcription factors on each others, gene expression levels. The reconstruction and analysis of these networks is a huge game in systems biology as the simulation of GRNs is capable of the explanation of system-level phenomena. Gene co-expression networks (GCNs) are the next important category in systems biology. Cytoscape is perhaps the most popular open source network analysis software tool. It has versatile network analysis tool set; therefore, it is an excellent complement to R and Bioconductor.