Abstract
Patients with coronavirus disease 2019 (COVID-19) might cause long-term burden of insomnia, while the common pathogenic mechanisms are not elucidated. The gene expression profiles of COVID-19 patients and healthy controls were retrieved from the GEO database, while gene set related with circadian rhythm was obtained from GeneCards database. Seventy-six shared genes were screened and mainly enriched in cell cycle, cell division, and cell proliferation, and 6 hub genes were found out including CCNA2, CCNB1, CDK1, CHEK1, MKI67, and TOP2A, with positive correlation to plasma cells. In the TF-gene regulatory network, NFYA, NFIC, MEF2A, and FOXC1 showed high connectivity with hub genes. This study identified six hub genes and might provide new insights into pathogenic mechanisms and novel clinical management strategies.
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Data availability
The datasets analyzed (GSE217948) during this study are publicly available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/), the original contributions presented in this study are included in the article/supplementary material, and further inquiries can be directed to the corresponding author.
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Acknowledgements
We gratefully acknowledge the contributions from the Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, GEO databases, and Genecards.
Funding
This research was supported by the National Natural Science Foundation of China (No: 82272034, 82102088) and the Capital’s Funds for Health Improvement and Research (No: 2020-2-2025).
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Contributions
Yanfeng Xu: Conceptualization, Methodology, Data curation, Software, Validation, Formal analysis, Visualization, Writing–original draft, Writing–review and editing.
Mingyu Zhang: Methodology, Writing-review and editing.
Guanyun Wang: Formal analysis, Data curation, Writing–review and editing.
Jigang Yang: Conceptualization, Funding acquisition, Project administration, Supervision, Writing–review and editing.
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ESM 1
Figure S1. Construction of co-expressed gene networks in dataset GSE217498. (A) Selection of soft threshold powers. (B) The constructed co-expression modules of COVID-19 related genes by WGCNA. (C) Module-trait association. Each row corresponded to a module feature, and each cell contained the correlation and the corresponding P value. (JPG 5483 kb)
ESM 2
Figure S2. (A) The correlation heat map of six hub genes. The area size and the color of circles represent the strength of the correlation between genes. (B) The heat map of six hub genes. Red represents high expression and blue represents low expression. (JPG 5316 kb)
ESM 3
Figure S3. (A-F) Bar plot of 6 identified hub genes in GSE217948. (G-L) Bar plot of 6 identified hub genes in GSE166253. ***: P < 0.001, *: P < 0.05, NS: P > 0.05. (JPG 8061 kb)
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Xu, Y., Zhang, M., Wang, G. et al. Identification of six genes associated with COVID-19-related circadian rhythm dysfunction by integrated bioinformatic analysis. Funct Integr Genomics 23, 282 (2023). https://doi.org/10.1007/s10142-023-01198-7
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DOI: https://doi.org/10.1007/s10142-023-01198-7