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Dear Dr. Ren,
The manuscript is now been accepted.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
Good
Good
Novel. Good
Congratulations! The authorshave satisfactorily answered all my concerns. The manuscript is very good and should be published.
Dear Dr. Ren,
The manuscript has been reviewed by two experts in the field. While one reviewer has accepted the manuscript, the other reviewer has raised significant concerns that need to be addressed. Please look at the suggestions pointed out by reviewer 2 and make the changes in the manuscript accordignly.
Clear and unambiguous and language is appropriate.
Sufficient field background and references
Figures and structured articles
Articles fit in Aims and scope of the Journal
Research question is improved in revised manuscript.
Investigation in details.
Methods described.
Findings are well defined. All data have been provided. Conclusions are well stated.
Author address my concerns.
The language can be made better
The question is well defined. The GSEA has made this manuscript better.
Conclusions could have been better stated.
This reviewer is of the opinion that the authors have done a good job with the rebuttal. However, though not fully agreeing with the other reviewer's comments about the research not being entirely novel, I feel that the conclusions of this manuscript can be made much better.
1) The strength of this manuscript is in the microRNAs prediction. Hence, I would suggest the authors to expand greatly on the ROC curve prediction and microRNA validation.
2) I would highly recommend running a few Western blots for protein validation
3) Please expand the discussion to put more focus on the microRNA validation and the results from the Western Blots (if run) from point 2
Dear Dr. Ren,
Your manuscript has been reviewed by two reviewers. Reviewers have some major concerns regarding the experimental design especially reviewer 1. Please check the comments and revise the manuscript accordingly.
[# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title) #]
English language is a concern throughout the manuscript. Another point is consistency of writing and use of terminology.
References aren't appropriately used.
Introduction is not well connected.
No original research.
No gene enrichment analysis was performed.
Research question was not well defined.
There is no rigorous investigation performed.
No novelty, this type of reports already published. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657850/).
Results were not interpreted and explanatory.
This is just use of bioinformatic tools study. Author only used qRT PCR to validate the genes but not western blots for their protein products.
The manuscript titled "Identification of diagnostic genes and vital
microRNAs involved in rheumatoid arthritis: based on
data mining and experimental verification" has been written well. There are very few grammatical errors in the manuscript with sufficient literature review provided. The data analysis and representation is adequate. The authors have missed to add the findings of a) Clin Exp Rheumatol. Jul-Aug 2017;35(4):586-592. Epub 2017 Jan 27.; b) Zhu X, Wu L, Mo X, et al. Identification of PBMC-expressed miRNAs for rheumatoid arthritis. Epigenetics. 2020;15(4):386-397. doi:10.1080/15592294.2019.1676613. The authors should consider including them in the discussion.
The experimental design is well planned to address the hypothesis with well defined objectives. There is adequate information for the repetition of the experiment by others.
The findings are novel for the biomarkers although there are reports on the miRNAs involved in RA patients. The conclusions are well supported with the findings of the study. The authors should validate a few of the miRNAs for functional role in regulating the inflammatory genes mentioned in the study as a functional validation of the study.
The authors have mentioend that the highly altered pathways belong to inflammation and cell-cell adhesion but they have not validated any gene for the cell-cell adhesion pathway or looked into its miRNA regulation. Why?
The authors should rectify the grammatical errors and space between the words in the manuscript.
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