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Prognostic significance of the Cdk5 gene in breast cancer: an in silico study

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Abstract

Cyclin-dependent kinase 5 (Cdk5) functions as a tumor promoter in various types of cancer. Cdk5 is overexpressed in breast cancer patients. The prognostic significance of the Cdk5 gene and its expression in breast cancer were analyzed using various bioinformatic tools. Cdk5 gene expression in different breast cancer subtypes was analyzed using the Oncomine, UALCAN, and bcGenExMiner v4.2 websites. The correlation between Cdk5 mRNA expression and promoter methylation was established using TCGA datasets from the UCSC Xena and UALCAN websites. The relationship between Cdk5 promoter methylation and different clinicopathological parameters in breast cancer patients was determined using UALCAN. Cdk5 expression is associated with various clinicopathological parameters, such as estrogen receptor, progesterone receptor, the basal-like subtype, and triple-negative breast cancer, which was analyzed using bcGenExMiner v4.2. Kaplan–Meier plotter revealed high Cdk5 expression and poor survival in breast cancer patients. In addition, a list of genes that are coexpressed with Cdk5 in breast cancer was identified from the UALCAN website. From that list, we observed that Fas-activated serine/threonine kinase (FASTK) has a predominant positive correlation with Cdk5 in breast cancer. The UCSC Xena and bcGenExMiner v4.2 websites were used to confirm the correlation between Cdk5 and FASTK. Cdk5 overexpression might induce malignancies and is associated with a poor prognosis in breast cancer patients through FASTK. Therefore, Cdk5 might act as a biomarker to predict the prognosis of breast cancer.

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Author notes

  1. Nafisa Ferdousi Lisany, Mohammad Abu Hena Mostofa Jamal and Hea-Jong Chung have contributed equally to this work.

Authors and Affiliations

  1. Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh

    Nafisa Ferdousi Lisany & Md. Shahedur Rahman

  2. Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh

    Mohammad Abu Hena Mostofa Jamal

  3. Department of Biomedical Sciences, Chonbuk National University Medical School, Chonbuk National University, Jeonju, South Korea

    Hea-Jong Chung & Seong-Tshool Hong

  4. Gwangju Center, Korea Basic Science Institute, Gwangju, South Korea

    Hea-Jong Chung

Authors
  1. Nafisa Ferdousi Lisany
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  2. Mohammad Abu Hena Mostofa Jamal
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  3. Hea-Jong Chung
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  4. Seong-Tshool Hong
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  5. Md. Shahedur Rahman
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Correspondence to Seong-Tshool Hong or Md. Shahedur Rahman.

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Supplementary Figure 1

(A) Heat map of Cdk5 expression and DNA methylation status, (B) Cdk5 expression in different breast cancer DNA methylation clusters (PDF 132 kb)

Supplementary material 2 (DOCX 20 kb)

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Lisany, N.F., Jamal, M.A.H.M., Chung, HJ. et al. Prognostic significance of the Cdk5 gene in breast cancer: an in silico study. Netw Model Anal Health Inform Bioinforma 9, 19 (2020). https://doi.org/10.1007/s13721-020-0225-1

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  • DOI: https://doi.org/10.1007/s13721-020-0225-1

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