Predicting the Pro-Longevity or Anti-Longevity Effect of Model Organism Genes with New Hierarchical Feature Selection Methods

IEEE/ACM Trans Comput Biol Bioinform. Mar-Apr 2015;12(2):262-75. doi: 10.1109/TCBB.2014.2355218.


Ageing is a highly complex biological process that is still poorly understood. With the growing amount of ageing-related data available on the web, in particular concerning the genetics of ageing, it is timely to apply data mining methods to that data, in order to try to discover novel patterns that may assist ageing research. In this work, we introduce new hierarchical feature selection methods for the classification task of data mining and apply them to ageing-related data from four model organisms: Caenorhabditis elegans (worm), Saccharomyces cerevisiae (yeast), Drosophila melanogaster (fly), and Mus musculus (mouse). The main novel aspect of the proposed feature selection methods is that they exploit hierarchical relationships in the set of features (Gene Ontology terms) in order to improve the predictive accuracy of the Naïve Bayes and 1-Nearest Neighbour (1-NN) classifiers, which are used to classify model organisms' genes into pro-longevity or anti-longevity genes. The results show that our hierarchical feature selection methods, when used together with Naïve Bayes and 1-NN classifiers, obtain higher predictive accuracy than the standard (without feature selection) Naïve Bayes and 1-NN classifiers, respectively. We also discuss the biological relevance of a number of Gene Ontology terms very frequently selected by our algorithms in our datasets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Bayes Theorem
  • Caenorhabditis elegans / genetics
  • Cellular Senescence / genetics*
  • Computational Biology / methods*
  • Data Mining / methods*
  • Databases, Genetic
  • Drosophila melanogaster / genetics
  • Gene Ontology
  • Mice
  • Models, Genetic*
  • Saccharomyces cerevisiae / genetics