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

Wenjian Xu1, Yang Cao2, Ziwei Xie3

  • 1Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Street, Haidian District, Beijing, 100850, China.

BMC Bioinformatics
|May 20, 2017
PubMed
Summary

NFPscanner is a new web server that helps biologists analyze gene networks. It quantitatively compares biological network functions, offering insights into unfamiliar pathways and molecular interactions.

Keywords:
Network decipheringNetwork fingerprintOnline interactive analysisPathway analysis

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Biological pathways represent diverse knowledge, including genetic interactions, metabolic reactions, and regulatory relationships.
  • Omics data enables the construction of context-specific molecular networks.
  • Current tools lack standardized methods for quantitative comparison of biological network functions.

Purpose of the Study:

  • To develop a standardized tool for quantitative and prompt comparison of multiple biological network functions.
  • To provide biologists with a user-friendly platform for deciphering gene networks and gaining insights into unfamiliar pathways.

Main Methods:

  • Development of NFPscanner, a web server based on the network fingerprint framework.
  • Integration of 7 pathway databases, 4 algorithms, and 2 visualization modules.
  • Implementation of three network analysis types: Fingerprint, Alignment, and Enrichment.

Main Results:

  • NFPscanner enables deciphering gene networks and highlighting inherent pathway modules.
  • The tool facilitates discovery of functional associations by aligning gene networks.
  • NFPscanner calculates and visualizes gene ontology (GO) and pathway enrichment for genes within networks.

Conclusions:

  • NFPscanner is an open-source web server for non-commercial use.
  • The tool provides an interactive platform for exploring gene network functions.
  • NFPscanner addresses the need for efficient biological network analysis and comparison.