Classifying aging genes into DNA repair or non-DNA repair-related categories

Yaping Fang, Xinkun Wang, Elias K. Michaelis, Jianwen Fang*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Scopus citations

Abstract

The elderly population in almost every country is growing faster than ever before. However, our knowledge about the aging process is still limited despite decades of studies on this topic. In this report, we focus on the gradual accumulation of DNA damage in cells, which is a key aspect of the aging process and one that underlies age-dependent functional decline in cells, tissues, and organs. To achieve the goal of discriminating DNA-repair from non-DNA-repair genes among currently known genes related to human aging, four machine learning methods were employed: Decision Trees, Naïve Bayes, Support Vector Machine, and Random Forest (RF). Among the four methods, the RF algorithm achieved a total accuracy (ACC) of 97.32% and an area under receiver operating characteristic (AUC) of 0.98. These estimates were based on 18 selected attributes, including 10 Gene Ontology and 8 Protein-Protein Interaction (PPI) attributes. A predictive model built with only 15 PPI attributes achieved performance levels of ACC= 96.56% and AUC=0.95. Systems biology analyses showed that the features of these attributes were related to cancer, genetic, developmental, and neurological disorders, as well as DNA replication/ recombination/repair, cell cycle, cell death, and cell function maintenance. The results of this study indicate that genes indicative of aging may be successfully classified into DNA repair and non-DNA repair genes and such successful classification may help identify pathways and biomarkers that are important to the aging process.

Original languageEnglish (US)
Title of host publicationIntelligent Computing Theories and Technology - 9th International Conference, ICIC 2013, Proceedings
Pages20-29
Number of pages10
DOIs
StatePublished - 2013
Event9th International Conference on Intelligent Computing, ICIC 2013 - Nanning, China
Duration: Jul 28 2013Jul 31 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7996 LNAI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other9th International Conference on Intelligent Computing, ICIC 2013
Country/TerritoryChina
CityNanning
Period7/28/137/31/13

Keywords

  • Aging
  • Classification
  • DNA-repair
  • Feature selection
  • Random Forest

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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