Machine learning-based identification of genetic interactions from heterogeneous gene expression profiles

Chihyun Park, Jung Rim Kim, Jeongwoo Kim, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

The identification of disease-related genes and disease mechanisms is an important research goal; many studies have approached this problem by analysing genetic networks based on gene expression profiles and interaction datasets. To construct a gene network, correlations or associations among pairs of genes must be obtained. However, when gene expression data are heterogeneous with high levels of noise for samples assigned to the same condition, it is difficult to accurately determine whether a gene pair represents a significant gene–gene interaction (GGI). In order to solve this problem, we proposed a random forest-based method to classify significant GGIs from gene expression data. To train the model, we defined novel feature sets and utilised various high-confidence interactome datasets to deduce the correct answer set from known disease-specific genes. Using Alzheimer’s disease data, the proposed method showed remarkable accuracy, and the GGIs established in the analysis can be used to build a meaningful genetic network that can explain the mechanisms underlying Alzheimer’s disease.

Original languageEnglish
Article numbere0201056
JournalPloS one
Volume13
Issue number7
DOIs
Publication statusPublished - 2018 Jul

Bibliographical note

Funding Information:
This research was supported by Next-Generation Information Computing Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT (NRF 2015M3C4A7065522).

Publisher Copyright:
© 2018 Park et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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