Network Analyst framework 

Meta-analysis of gene expression data sets is becoming more common to aid in identifying strong molecular signatures and acquiring insights into underlying biological processes. Because such studies are complex, advanced statistics and new visualization methodologies are required for rapid data comparison, interpretation, and hypothesis formulation. NetworkAnalyst is a comprehensive web-based application that allows bench researchers to do common and complicated meta-analyses of gene expression data using an easy-to-use online interface. NetworkAnalyst enables researchers to navigate sizeable complex gene expression data easily sets to determine important features, patterns, functions, and connections, leading to the generation of new biological hypotheses by combining well-established statistical procedures with innovative data visualization techniques.  

his protocol describes in detail how to use NetworkAnalyst to perform network analysis and visualization from gene lists, a meta-analysis of gene expression data while taking into account multiple metadata parameters, and a meta-analysis of multiple gene expression data sets. NetworkAnalyst is intended for use by biologists rather than specialized bioinformaticians. The entire process may be completed in 1.5 hours. In comparison to other similar web-based applications, NetworkAnalyst provides a distinct visual analytics experience that allows data analysis in the context of protein-protein interaction networks, heatmaps, or chord diagrams. All of these analytical approaches give statistical and functional proof to the user. 

References 

Xia, J., Gill, E. & Hancock, R. NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.  Nat Protoc 10, 823–844 (2015).