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Bioinform Biol Insights. 2017 Dec 13;11:1177932217746991. doi: 10.1177/1177932217746991. eCollection 2017.

Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes.

Author information

1
Division of Biotechnology, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran.
2
Department of Biology, Friedrich Alexander University of Erlangen-N├╝rnberg, Erlangen, Germany.
3
Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Abstract

Background:

Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. This study aims to investigate the circadian expression of a list of human oncogenes and TSGs.

Methods:

A bioinformatic analysis was conducted on a gene library comprising 120 genes to investigate the circadian expression of human oncogenes and TSGs. To achieve this purpose, the genotranscriptomic data were retrieved from COSMIC and analyzed by R statistical software. Furthermore, the acquired data were analyzed at the transcriptomic and proteomic levels using several publicly available databases. Also, the significance of all analyses was confirmed statistically.

Results:

Altogether, our results indicated that 7 human oncogenes/TSGs may be expressed and function in a circadian manner. These oncogenes/TSGs showed a circadian expression pattern at CircaDB database and associated with at least one of the circadian genes/CCGs based on both genotranscriptomic and correlation analyses.

Conclusions:

Although 4 of 7 finally outputted genes have been previously reported to be clock controlled, heretofore there is no report about the circadian expression of 3 other genes. Considering the importance of oncogenes/TSGs in the initiation and progression of cancer, further studies are suggested for the identification of exact circadian expression patterns of these 3 human oncogenes/TSGs.

KEYWORDS:

Oncogenes; bioinformatic analysis; circadian expression; tumor suppressor genes (TSGs)

Conflict of interest statement

Declaration of conflicting interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

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