Systematic and Integrative Analysis of Proteomic Data using   Bioinformatics Tools
  The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network models have facilitated a shift from the study of evolutionary conservation between individual gene and gene products towards the study of conservation at the level of pathways and complexes. Recent work has revealed much about chemical reactions inside hundreds of organisms as well as universal characteristics of metabolic networks, which shed light on the evolution of the networks. However, characteristics of individual metabolites have been neglected in this network. The current paper provides an overview of bioinformatics software used in visualization of biological networks using proteomic data, their main functions and limitations of the software. 
Rashmi Rameshwari and T. V. Prasad
cs.CE