Machine learning-based predictions of dietary restriction associations across ageing-related genes

Gustavo Daniel Vega Magdaleno, Vladislav Bespalov, Yalin Zheng, Alex A. Freitas, Joao Pedro Lourenco Rocha De Magalhaes

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Abstract

Background: Dietary restriction (DR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identification of novel DR-related genes and DR-related genetic features.

Results: This work used a Machine Learning (ML) approach to classify ageing-related genes as DR-related or NotDR-related using 9 different types of predictive features: PathDIP pathways, two types of features based on KEGG pathways, two types of Protein–Protein Interactions (PPI) features, Gene Ontology (GO) terms, Genotype Tissue Expression (GTEx) expression features, GeneFriends co-expression features and protein sequence descriptors. Our findings suggested that features biased towards curated knowledge (i.e. GO terms and biological pathways), had the greatest predictive power, while unbiased features (mainly gene expression and co-expression data) have the least predictive power. Moreover, a combination of all the feature types diminished the predictive power compared to predictions based on curated knowledge. Feature importance analysis on the two most predictive classifiers mostly corroborated existing knowledge and supported recent findings linking DR to the Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) signalling pathway and G protein-coupled receptors (GPCR).

We then used the two strongest combinations of feature type and ML algorithm to predict DR-relatedness among ageing-related genes currently lacking DR-related annotations in the data, resulting in a set of promising candidate DR-related genes (GOT2, GOT1, TSC1, CTH, GCLM, IRS2 and SESN2) whose predicted DR-relatedness remain to be validated in future wet-lab experiments.

Conclusions: This work demonstrated the strong potential of ML-based techniques to identify DR-associated features as our findings are consistent with literature and recent discoveries. Although the inference of new DR-related mechanistic findings based solely on GO terms and biological pathways was limited due to their knowledge-driven nature, the predictive power of these two features types remained useful as it allowed inferring new promising candidate DR-related genes.

Original languageEnglish
Article number10
Number of pages28
JournalBMC Bioinformatics
Volume23
Issue number1
Early online date4 Jan 2022
DOIs
Publication statusPublished - Dec 2022

Bibliographical note

Funding Information:
This work was supported by a Biotechnology and Biological Sciences Research Council (BB/R014949/1) to J.P.M., a Wellcome Trust Grant (208375/Z/17/Z) to J.P.M., a Leverhulme Trust research Grant (RPG-2016-015) to J.P.M. and A.A.F., a CONACyT sponsorship (2019-000021-01EXTF-00468) to G.D.V.M, and an University of Guadalajara loan (V/2020/449) to G.D.V.M..

Publisher Copyright:
© 2021, The Author(s).

Keywords

  • Ageing
  • Dietary restriction
  • Machine learning

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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