Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway

PLoS One. 2014 Sep 10;9(9):e107202. doi: 10.1371/journal.pone.0107202. eCollection 2014.

Abstract

Cancer is a serious disease that causes many deaths every year. We urgently need to design effective treatments to cure this disease. Tumor suppressor genes (TSGs) are a type of gene that can protect cells from becoming cancerous. In view of this, correct identification of TSGs is an alternative method for identifying effective cancer therapies. In this study, we performed gene ontology (GO) and pathway enrichment analysis of the TSGs and non-TSGs. Some popular feature selection methods, including minimum redundancy maximum relevance (mRMR) and incremental feature selection (IFS), were employed to analyze the enrichment features. Accordingly, some GO terms and KEGG pathways, such as biological adhesion, cell cycle control, genomic stability maintenance and cell death regulation, were extracted, which are important factors for identifying TSGs. We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Adhesion / genetics
  • Cell Cycle Checkpoints / genetics
  • Cell Death / genetics
  • Computational Biology
  • Data Mining
  • Gene Ontology*
  • Genes, Tumor Suppressor*
  • Genome, Human*
  • Genomic Instability
  • Humans
  • Metabolic Networks and Pathways / genetics*
  • Neoplasm Proteins / classification
  • Neoplasm Proteins / genetics*
  • Neoplasms / genetics*
  • Neoplasms / pathology

Substances

  • Neoplasm Proteins

Grants and funding

This work was supported by the National Basic Research Program of China (2011CB510102, 2011CB510101), the National Natural Science Foundation of China (31371335, 61202021, 61373028, 11371008, 81030015), Innovation Program of Shanghai Municipal Education Commission (12ZZ087, 12YZ120), the Shanghai Educational Development Foundation (12CG55) and the grant from “The First-class Discipline of Universities in Shanghai.” The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.