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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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PANEV: an R package for a pathway-based network visualization.

Valentino Palombo1, Marco Milanesi2,3, Gabriella Sferra4

  • 1Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, 86100, Campobasso, Italy.

BMC Bioinformatics
|February 8, 2020
PubMed
Summary

PANEV is a new R package for visualizing gene and pathway networks. It aids in analyzing complex genomic data by mapping interconnected pathways to identify candidate genes.

Keywords:
Data miningGenomic and transcriptomic analysisKEGGMolecular pathwaysPathway visualization

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Post-genomic and transcriptomic data analysis presents challenges in mining complex biological information.
  • Interconnected metabolic pathway networks are crucial for understanding complex biological phenomena and identifying trait-associated genes.

Purpose of the Study:

  • To introduce PANEV (PAthway NEtwork Visualizer), an R package designed for gene and pathway network visualization.
  • To facilitate the interpretation of functional profiles within gene clusters by visualizing interconnected pathways.

Main Methods:

  • PANEV utilizes KEGG database information to construct multi-level networks (1 to n) of interconnected pathways.
  • The package visualizes genes within these networks, highlighting upstream and downstream relationships.

Main Results:

  • PANEV provides a network graph visualization for interpreting gene functional profiles.
  • The R package enables the analysis of genomic or transcriptomic data without species constraints.

Conclusions:

  • PANEV is a versatile tool for researchers analyzing gene and pathway networks.
  • Users can customize network complexity by specifying candidate genes, target pathways, and the number of interconnected pathway levels.