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dna: An R package for differential network analysis.

Ryan Gill1, Somnath Datta2, Susmita Datta2

  • 1Department of Mathematics, University of Louisville, Louisville, KY 40292 USA.

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|June 27, 2014
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Summary
This summary is machine-generated.

The R package dna facilitates differential network analysis for genomic data, comparing gene networks across conditions. It offers tools for preprocessing, calculating gene connectivity, and performing permutation tests to identify significant network differences.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Differential network analysis identifies structural differences between biological networks under varying conditions.
  • The R package dna provides a comprehensive suite of tools for conducting such analyses on genomic data.

Purpose of the Study:

  • To introduce the R package dna for differential network analysis of gene-gene networks.
  • To offer flexible methods for preprocessing, scoring gene connectivity, and performing statistical tests.

Main Methods:

  • The dna package includes preprocessing functions for preparing network pairs.
  • It computes gene-gene connectivity scores using various statistical techniques.
  • Permutation tests are implemented to assess differences in gene connectivity and module structure.

Main Results:

  • The package enables the determination of differential gene connectivity between two networks.
  • It allows for the assessment of differences in connectivity for specific gene sets.
  • The analysis of overall module structure differences between networks is supported.

Conclusions:

  • The dna package provides a robust framework for differential network analysis in genomics.
  • Its adaptable methods and built-in options facilitate the identification of condition-specific network changes.