The use of Gene Ontology terms and KEGG pathways for analysis and prediction of oncogenes

Biochimica Et Biophysica Acta
Zhihao XingXiangyin Kong

Abstract

Oncogenes are a type of genes that have the potential to cause cancer. Most normal cells undergo programmed cell death, namely apoptosis, but activated oncogenes can help cells avoid apoptosis and survive. Thus, studying oncogenes is helpful for obtaining a good understanding of the formation and development of various types of cancers. In this study, we proposed a computational method, called OPM, for investigating oncogenes from the view of Gene Ontology (GO) and biological pathways. All investigated genes, including validated oncogenes retrieved from some public databases and other genes that have not been reported to be oncogenes thus far, were encoded into numeric vectors according to the enrichment theory of GO terms and KEGG pathways. Some popular feature selection methods, minimum redundancy maximum relevance and incremental feature selection, and an advanced machine learning algorithm, random forest, were adopted to analyze the numeric vectors to extract key GO terms and KEGG pathways. Along with the oncogenes, GO terms and KEGG pathways were discussed in terms of their relevance in this study. Some important GO terms and KEGG pathways were extracted using feature selection methods and were confirmed to be highly relat...Continue Reading

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Aug 4, 2016·Biochimica Et Biophysica Acta·Yudong Cai, Tao Huang
Feb 6, 2020·Experimental and Therapeutic Medicine·Luyao WangJia Liu
Apr 21, 2018·Interdisciplinary Sciences, Computational Life Sciences·Jieyuan DingShuaiqun Wang
Feb 9, 2019·Journal of Enzyme Inhibition and Medicinal Chemistry·Jie WuLei Song
Oct 17, 2019·Journal of Molecular Neuroscience : MN·Chengyuan DongSheng Fang
Jun 20, 2020·Journal of Cancer Research and Clinical Oncology·Jie LiuDong Wang
Oct 9, 2020·BioMed Research International·Ran ZhaoBo Zhou
Nov 17, 2020·Frontiers in Cellular and Infection Microbiology·Mohsin NawazJinlin Zhou
Jun 17, 2021·Genes and Environment : the Official Journal of the Japanese Environmental Mutagen Society·Linlin SaiCheng Peng
Jul 2, 2021·Evidence-based Complementary and Alternative Medicine : ECAM·Yu-Bao GongJian-Guo Liu

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