NFPscanner: a webtool for knowledge-based deciphering of biomedical networks

Abstract

Abstract Background Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis. They would benefit from the development of a standardized tool to compare functions of multiple biological networks quantitatively and promptly. Results To address this challenge, we developed NFPscanner, a web server for deciphering gene networks with pathway associations. Adapted from a recently reported knowledge-based framework called network fingerprint, NFPscanner integrates the annotated pathways of 7 databases, 4 algorithms, and 2 graphical visualization modules into a webtool. It implements 3 types of network analysis: Fingerprint: Deciphering gene networks and highlighting inherent pathway modules Alignment: Discovering functional associations by finding optimized node mapping between 2 gene networks Enrichment: Calculating and visualizing gene ontology (GO) and pathway enrichment for genes in networks Users can upload gene networks to NFPscanner through the web interface and then interactively explore the networks’ functions. Conclusions NFPscanner is open-source software for non-commercial use, freely accessible at http://biotech.bmi.ac.cn/nfs .

Keywords

• Network deciphering
• Pathway analysis
• Online interactive analysis
• Network fingerprint