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Editor
Loulia KouKou
Identification of key genes in SARS-CoV-2 patients on bioinformatics analysis (2020)
Hanming Gu, Gongsheng Yuan
This manuscript is rejected. This study looks at differentially expressed genes between patients with- and without coronavirus and the associated biological processes. Reported results include that several biological pathways are included in the development of COVID-19 and several other genes are critical for virus invasion and adhesion.
Major points: Comment #1 I can find the following papers by the same authors that applies the exact same type of analysis to different problems: • Identification of specific biomarkers and pathways in the synovial tissues of patients with osteoarthritis in comparison to rheumatoid arthritis https://www.biorxiv.org/content/10.1101/2020.10.22.340232v1.full.pdf • Identification of potential biomarkers and inhibitors for SARS-Cov-2 infection https://www.medrxiv.org/content/10.1101/2020.09.15.20195487v1.full.pdf • Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis https://www.biorxiv.org/content/10.1101/2020.08.18.256735v2
There are clear examples of sentences being rewritten, which I consider as plagiarism.
Comment #2 The work is clear to follow, but it feels like a report done in a course, not a scientific paper. The results are listed in a clear manner, but the table and figures repeat the same and does not deepen ones understanding of the results.
The results section should be reorganized, as it is very hard to read and comprehend all of the biological terms. Instead, I suggest using the tables and/or figures more and only highlight the most interesting findings in this section. Using the fold change values from table 1 could also make the results more interesting than just listing the terms.
Comment #3 The discussion only briefly links their results to patient cases in the US, but there is no statistical analysis done that can support these conclusions. Therefore, it is unclear whether these results can actually account for any observed trends in real life.
Minor points: Comment #4 The introduction section gives a good overview of the current status and how understanding which gene products are essential for the virus can improve treatment. It is very simply written but gets the point across. There are no references to studies that have analyzed differentially expressed genes in a similar manner and applied it to improve therapies.
Comment #5 There aren’t any references to papers that have done a similar analysis of differentially expressed genes on other diseases, which could make the study appear more solid than it does in its current state.
Overall recommendation: reject due to concerns about the authors duplicating their analysis work on different topics and the analysis does not support any novel findings.
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