Abstract
Biological network analysis is a powerful approach to gain systems-level understanding of patterns of gene expression in different cell types, disease states and other biological/experimental conditions. Three consecutive steps are required - identification of genes or proteins of interest, network construction and network analysis and visualization. To date, researchers have to learn to use a combination of several tools to accomplish this task. In addition, interactive visualization of large networks has been primarily restricted to locally installed programs. To address these challenges, we have developed NetworkAnalyst, taking advantage of state-of-the-art web technologies, to enable high performance network analysis with rich user experience. NetworkAnalyst integrates all three steps and presents the results via a powerful online network visualization framework. Users can upload gene or protein lists, single or multiple gene expression datasets to perform comprehensive gene annotation and differential expression analysis. Significant genes are mapped to our manually curated protein-protein interaction database to construct relevant networks. The results are presented through standard web browsers for network analysis and interactive exploration. NetworkAnalyst supports common functions for network topology and module analyses. Users can easily search, zoom and highlight nodes or modules, as well as perform functional enrichment analysis on these selections. The networks can be customized with different layouts, colors or node sizes, and exported as PNG, PDF or GraphML files. Comprehensive FAQs, tutorials and context-based tips and instructions are provided. NetworkAnalyst currently supports protein-protein interaction network analysis for human and mouse and is freely available at http://www.networkanalyst.ca.
Highlights
High-throughput omics technologies have enabled global measurement of biological molecules (DNA, RNA, proteins, metabolites, etc.) under various experimental conditions and disease states
Protein–protein interaction (PPI) networks have emerged as an important resource for understanding data from gene expression or proteomics experiments
We introduce NetworkAnalyst, a web-based user-friendly tool that integrates all essential steps of network analysis, and present the results through a powerful online visualization system
Summary
High-throughput omics technologies have enabled global measurement of biological molecules (DNA, RNA, proteins, metabolites, etc.) under various experimental conditions and disease states. There is a clear need for facile, pointand-click web-based tools that allow bench researchers to seamlessly move from their gene expression data to network analysis and visualization, without having to use and install multiple different tools. The current implementation allows analysis and rapid visualization of the resulting PPI networks from small to large size (100– 1000s nodes). Multiple nodes can be selected using the checkbox These features allow users to visualize all seed proteins or. Function Explorer allows users to perform functional enrichment analysis for currently highlighted nodes using different databases such as the GO, KEGG or Reactome pathway databases. When seed proteins from multiple datasets are projected to the network, users can choose to highlight those nodes from one particular data. We recommend using a computer with at least 2G RAM and 1280 × 800 screen resolution
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
