MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions

Kieu Trinh Do, David J.N.P. Rasp, Gabi Kastenmüller, Karsten Suhre, Jan Krumsiek

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Summary: Associations of metabolomics data with phenotypic outcomes are expected to span functional modules, which are defined as sets of correlating metabolites that are coordinately regulated. Moreover, these associations occur at different scales, from entire pathways to only a few metabolites; an aspect that has not been addressed by previous methods. Here, we present MoDentify, a free R package to identify regulated modules in metabolomics networks at different layers of resolution. Importantly, MoDentify shows higher statistical power than classical association analysis. Moreover, the package offers direct interactive visualization of the results in Cytoscape. We present an application example using complex, multifluid metabolomics data. Due to its generic character, the method is widely applicable to other types of data. Availability and implementation: https://github.com/krumsieklab/MoDentify (vignette includes detailed workflow). Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)532-534
Number of pages3
JournalBioinformatics (Oxford, England)
Volume35
Issue number3
DOIs
Publication statusPublished - 1 Feb 2019

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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