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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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ProphTools: general prioritization tools for heterogeneous biological networks.

Carmen Navarro1, Victor Martínez1, Armando Blanco1

  • 1Department of Computer Science and Artificial Intelligence, University of Granada, Granada, Spain.

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|November 30, 2017
PubMed
Summary
This summary is machine-generated.

ProphTools is a new open-source tool for analyzing complex biological networks. It offers flexible prioritization for user-defined data, proving effective for long noncoding RNA-disease associations.

Keywords:
heterogeneous networkslong noncoding RNAsnetwork analysisprioritization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Network Science

Background:

  • Biological data analysis relies heavily on network representations.
  • Existing network analysis methods often lack flexibility for user-defined data and specific biological entity types.
  • There is a need for adaptable tools to extract knowledge from complex biological networks.

Purpose of the Study:

  • To introduce ProphTools, a flexible open-source command-line tool for network prioritization.
  • To enable analysis of user-defined heterogeneous networks with arbitrary entity types and interconnections.
  • To demonstrate ProphTools' utility in biological prioritization tasks, including long noncoding RNA-disease association.

Main Methods:

  • Developed ProphTools, a flexible open-source prioritization tool.
  • Implemented a prioritization algorithm combining Flow Propagation and weighted propagation methods.
  • Enabled user-defined heterogeneous network models and cross-validation for optimal configuration selection.

Main Results:

  • ProphTools successfully performs prioritization on heterogeneous networks.
  • The tool integrates Flow Propagation and weighted propagation algorithms for robust analysis.
  • A case study demonstrated ProphTools' effectiveness in long noncoding RNA-disease prioritization.

Conclusions:

  • ProphTools offers unparalleled flexibility for network prioritization compared to existing tools.
  • The software enables researchers to analyze custom heterogeneous networks.
  • ProphTools achieves high performance in lncRNA-disease prioritization, matching specialized tools.