NetConfer: a web application for comparative analysis of multiple biological networks
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NetConfer: a web application for comparative analysis of multiple biological networks Sunil Nagpal1, Krishanu Das Baksi1, Bhusan K. Kuntal1,2,3* and Sharmila S. Mande1*
Abstract Background: Most biological experiments are inherently designed to compare changes or transitions of state between conditions of interest. The advancements in data intensive research have in particular elevated the need for resources and tools enabling comparative analysis of biological data. The complexity of biological systems and the interactions of their various components, such as genes, proteins, taxa, and metabolites, have been inferred, represented, and visualized via graph theory-based networks. Comparisons of multiple networks can help in identifying variations across different biological systems, thereby providing additional insights. However, while a number of online and stand-alone tools exist for generating, analyzing, and visualizing individual biological networks, the utility to batch process and comprehensively compare multiple networks is limited. Results: Here, we present a graphical user interface (GUI)-based web application which implements multiple network comparison methodologies and presents them in the form of organized analysis workflows. Dedicated comparative visualization modules are provided to the end-users for obtaining easy to comprehend, insightful, and meaningful comparisons of various biological networks. We demonstrate the utility and power of our tool using publicly available microbial and gene expression data. Conclusion: NetConfer tool is developed keeping in mind the requirements of researchers working in the field of biological data analysis with limited programming expertise. It is also expected to be useful for advanced users from biological as well as other domains (working with association networks), benefiting from provided ready-made workflows, as they allow to focus directly on the results without worrying about the implementation. While the web version allows using this application without installation and dependency requirements, a stand-alone version has also been supplemented to accommodate the offline requirement of processing large networks. Keywords: Biological networks, Network comparison, Interaction networks, Visualization, Bioinformatics
Background Networks provide one of the means to construct a theoretical model for representing the relationships between the entities of complex systems. Such representations often help visualizing in a convenient way the relationships as well as capture the concepts for an improved * Correspondence: [email protected]; [email protected] 1 Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411 013, India Full list of author information is available at the end of the article
understanding. Networks can also be used to transform a generic problem into a mathematical model represented by graphs. Consequently, methods and tools used for solving a graph theory p
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